I also noticed when I was instead monitoring the audio through Direct Monitor that just opening up Logic, the application, causes this weird issue to happen.

Lets establish a few things.

First, the MODX sends analog audio to the Main L&R Analog Outputs... and It sends digital audio to the Main L&R USB (Digital) Outputs. Both streams are happening. It is your responsibility to choose one or the other (never both) to monitor.

Direct Monitor - literally means the signal path that is the MODX connected with two 1/4" cables to your studio monitors via the Main L&R Analog Outputs. The signal travels this route with or without the computer when Direct Monitor is On. If you turn Direct Monitor Off, the MODX is no longer sending signal *directly* to the speakers. It will then only be sending the digital stream to the computer.

When you open Logic the audio that is traveling via the USB cable arrives in computer. You must route it to the Audio Interface ... you do so by creating an Audio Track which must be set to go back to the MODX in order for you to hear it... this means setting up the Main Stereo Out of the DAW, Logic Pro, to the MODX via USB.

All right, I've managed to capture the USB signal as bounceable audio in Logic, I hadn't ticked the "Input Monitoring" on the audio tracks. I still get this issue where the sound/character of the performance is altered, it seems to happen semi-randomly, such as if I create a new software instrument track, or if i just even select a track such as the MODX Connect track then return to the midi track I intend to record on. I'm able to return the sound back to normal by just changing performance back and forth again, but it's a little tedious to have to do frequently. Is there any reason this might be happening?

Yes, there is. Overall, these things will keep 'happening' while you are unclear on the routing scenario. It is complex, that's the nature of the beast. Nothing is "semi-randomly" happening, everything happens for a specific reason...there is cause and effect.

Monitoring is what you choose to listen to. Trust me on this (I used to teach audio engineering) and what that taught me, more important than learning the routing... is that when someone is on the "learning curve" the most common stumbling block comes from thinking that equates what you're hearing with what you are recording. Often they are two separate signal paths.

In fact, in most Pro recording scenarios there are two signal paths... one you Monitor, the other you Record. You attempt to make these two signal paths as 'exactly the same' as is possible so that when you playback the recording, it sounds like it did when you sent it to the recorder.

In other words: You do not, technically speaking, listen to the recording as it is being made. You listen to the signal before it is recorded by the computer/recorder.
Back in the days of magnetic tape, it was the same... in the Control Room you listened to the "Monitor mix" - a subjective blend of the instrument inputs. Meanwhile, what was being sent to the Multi-Track recorder was an individually gain optimized signal per Input channel.

The subjective Monitor mix was a peek at what the end product would sound like once finalized. Generally, reverb is not initially recorded, but it is used in the Monitor mix... the Monitor mix was the equivalent of 'virtual audio' today... it's a glimpse of the finished product.
The scientific mix, the one going to the Multi-Track, meticulously gain staged, made a terrible musical balance to listen to... why? Because every Input was optimized for level. No frills like reverb so everything maximized and devoid of reverberation. Sounds like a band that doesn't know how to play *together*... imagine everyone trying to play as loud as they can all at the same time.... makes for a great recording level wise, but sounds like a musical argument where everyone thinks they're the star!

The two signal paths exist simultaneously. Knowing where you are tapping in to Monitor is not, cannot, and should not be guesswork. Once you become comfortable with the Signal Flow, trust me, you'll smile when an issue comes up... because you'll have the 'know how' to FIX IT! When that happens, you'll know.

First, thing to realize is: hearing (monitoring) is not a prerequisite to recording. Recording can take place in the absence of the signal path that feeds a pair of speakers. In my Audio class, during a recording, I'd stage an incoming phone call... musicians are in the studio, tape is rolling, phone rings... the student engineer is tasked with turning down the music in the Control Room without interrupting the recording.

Stressful moment, some freeze. Some panic and ruin the recording... but *everyone* learns that turning down the monitors does not affect the recording. Turning down items on the signal path going to the recorder would be WRONG. Turning down items going to the Monitor mix is fine, no one knows but us in the Control Room.
The moment was easy for some students, but a big "eureka!" moment for others. They had been equating what they hear with what was being recorded.

We spent time learning to set levels separately from hearing. Simply to make the point... the signal arrives at the meter (and can be actually recorded) without being routed through the speakers! Separate signal paths. And the student learned that Soloing an Input does not interrupt the other channels being recorded... because the Solo bus simply selects what gets routed to the monitor speakers without disturbing any other signal path. Another eureka moment.

What you are dealing with also includes MIDI that makes no sound until it triggers a Tone Generator... at that point the Tone Generator produces audio... an analog audio path that heads to the speakers, and a digital path that heads to the computer, to the DAW, and then back to the audio interface and finally to the speakers.

One path gets there at the 'speed of light' (zero latency), the other travels to the computer, is documented, then sent to D-to-A before going to the speakers. This arrives slightly later than the speed of light path.

Only the speakers in this scenario make SOUND. Sound is st the end of the chain... and is always analog.
Volume is analog... it's the manifestation of sound - molecules bouncing off each other... in this case air molecules.
Gain and Level are manifestations of the work a signal can do. They are not sound, but can influence the resulting Volume of a sound... but that is not a requirement.

You can choose to listen (monitor) at different points... if you don't choose, you'll hear both... it will sound strange... just like when two things are sounding with the same program a few milliseconds apart. That is not wrong, it is correct that both signals exist, what's wrong is operator error... you need to Monitor just one of them. Turning the signal down after it's been documented on the computer will not effect what was recorded ... knowing this is everything - you can verify with Metering that recording is happening... but because it is several milliseconds late, you can safely MUTE that signal... and choose to Monitor the "live" signal, it's playing speed of light.

Hope that helps... it is not semi-random. Each scenario can be explained by signal flow. It is complicated with MIDI because MIDI has its own back and forth that can be taking place all before any audio is even generated.

Suggestion... instead of jumping around. Attempt to master one type of recording at a time. Try following the signal flow in each scenario.
Btw- The MODX CONNECT item is not a Track - understand that highlighting it is simply changing away from whatever you had selected. You cannot record anything to the MODX CONNECT lane. The *selected* item is determines what you are in communication with. Think about it, Local Control is Off when recording MIDI. If you select a MIDI Track you are in communication with the instrument and channel defined by that Track, if that happens to be a MODX MIDI Track it will communicate with that Part on the channel of the Track... if it happens to be a plugin synth it will communicate with that synth.

At this point I'm still at a loss as to why the sound quality of any given patch becomes incredibly distorted upon opening up Logic. Is there any way of troubleshooting this, I believe I have followed the steps accurately now and have audio feeding through to an audio channel, as per the MODX template that gets installed goes.

Trying to re-initialise all data does nothing, I really can't tell what's causing this issue.

I would tend to guess that something in your Logic setup is sending MIDI to MODX which is altering the sound. If I were to try to debug this, I would place a MIDI monitor plugin on the MIDI track(s) you have connected to MODX and look to see if the DAW is sending anything or not. Alternatively, you could go into MODX and turn off MIDI receive of many of the CC values that would be altering the sound.

If your Performance has motion control or ARPs - these are other possibilities which you can turn off as well.