Pedalmania, me thinks...Controllers like cc007 and cc011 are fixed to control everything on the Channel. They are the most to difficult to manage because they affect the entire Channel (or not, you can opt to ignore it). These are not your only option to control levels of things independently. cc004 Foot Control can be programmed to do different things to different devices on the same channel - because it is programmed within the receiving device. cc004 has no predetermined function - so you can set it any number of control destinations.

Also when working multiple keyboards - often the easiest way to control the volume of each independently is to use a Foot Controller per device - once you have multiple devices all receiving on from one controller - you almost have to try the routing to see what will work. I could not really follow what you are doing well enough to tell you if it works. MIDI works consistently by a set of rules.

You ask if MIDI that is sent "Thru" a computer DAW is going to work the same way... well, no, its not. A typical DAW software like Cubase, works with MIDI by receiving data coming in - no matter what MIDI channel the source. The MIDI channel you see on the Track in Cubase is the channel that the TRACK Rechannelizes the data on going OUT. Remember MIDI Note-On Events includes the MIDI Channel... So while Cubase receives whatever channel is coming in, it very specifically rechannelizes all data on the way out.

So if you activate a Cubase MIDI track with Track Inspector set to Channel = 12, it matters not what MIDI channel your keyboard sends into the Track, what echoes back is going to be rechannelized on MIDI Channel 12. Local Control is OFF so what you hear respond is the PART or PARTs set to Channel 12.

If you understand the MIDI IN and MIDI OUT of all of this and you are using Cubase you can setup to have Cubase rechannelize a single source to multiple devices on different Ports and Channels (you can activate more than one MIDI Track with Cubase).

You can get as complicated with MIDI as your understanding of the INs and OUTs allows.
And when it comes to controlling volumes of different devices on different MIDI Ports, from one controller... you are making this up as YOU go along. Don't think that 'everybody' does or wants to do what you are doing. The best thing you can do is have a theory based on your knowledge of how MIDI should work and go for it.

I suggest you look for other options beyond cc007 and cc011 since they are so rigid in their purpose universally. Only you know what you are trying to accomplish. Keep it simple - simple is always better.

You will not have to worry about how to make a tone engine ignore universal cc's if you program your Motif XF with cc004. You can have cc004 do something different in the external devices or nothing at all... depending on the programmability of your external device.