Yes, templates will change:

Source: Montage reference manual -- annotations for MODX

Audio Settings:
A/D Input Gain
Main L&R Gain
Assign L&R Gain (Montage only - not for MODX)
USB Main L&R Gain
USB 1-30 Gain (MODX is USB 1-8 gain)
Direct Monitor Switch
MIDI Settings
MIDI In/Out
Local Control
Arp MIDI Out
MIDI Sync
Clock Out
Receive/Transmit Sequencer Control
Controller Reset
FS CC Number
Super Knob CC Number (Added per MODX ref manual - applies to both Montage+MODX)
Scene CC Number (Added per MODX ref manual - applies to both Montage+MODX)
Part Output Settings
Part 1-16 Output Select
A/D In Output Select
Digital In Output Select

The footswitch setting is underlined.

Which also means that if you make a custom template - the FS CC Number can be saved in your custom template so it sets it to your setting.

Oversight or not - these buttons change all of the above parameters to something possibly other than what you would otherwise want.

This is a strange issue that seems like a pretty big oversight. I want the assignable FS to do Live Set+. No problem, I can easily set that up. However, I also want to use the quick setup templates for MIDI/audio DAW recording. Now here's the issue: Whenever I have used one of these templates and switch back to Standalone mode, the FS assignment changes back to the default (Arp switch I believe). Able while the three recording templates can be changed, the standalone template cannot. So every time I switch back to it I have to remember to change the FS assignment. A minor inconvenience, sure, but an annoying one. And forgetting to do it before a live performance could have dire consequences.

This seems like a pretty big oversight, or...? Am I missing something here?

What you have stated is true. Tapping the “Standalone” Quick Setup option returns the Utility mode setting to the out-of-the-box factory defaults. This is always true.

However, and this is what you are missing, each USER File (.X8U) that you make is where your custom configuration for your Utility Settings are stored. When you are working with a computer, as you understand, you have three customizable QUICK SETUP locations to Name and Store your own configurations.

When you complete work with the computer and are preparing to go perform a live gig, make sure your personal preferences for your Utility Mode Settings like the FS ASSIGN, the Super Knob CC, the Scene CC, MIDI Clock, Direct Monitoring etc., etc., etc., are all set the way that you need for the Gig.

You will do this by loading a USER FILE - that is where *your* settings are stored and retrieved.
You probably Load a file to get ready for your gig — make sure your User File contains your preferences for FS ASSIGN and all other Utility Settings you’ll need to play without a computer connected.

Even if you are using Library “Live Sets”, before any gig, get in the habit of restoring a USER FILE (.X8U) it automatically restores *your* personal settings.
When you outgrow the factory defaults or you simply wish to use your own custom settings, you have two choices:
__ Load you own settings from one of your own User File — because among all the other things a .X8U File saves - it saves your preference for each Utility Mode Setting
__ rewrite one of the three built-in Quick Setup Templates to represent your own “Standalone” status... you can name it “My Standalone”

Either way... your Utility Settings (which includes both the FS ASSIGN and the three QUICK SETUPs) are stored in each User File *you* make. So if you come up with your own custom Quick Setup configurations, they will be stored in *your* User Files

Make a USER File for going to gig...
Make a USEr File for going to the studio...

Warning: when you initialize your data, things will return to Factory (out-of-the-box) condition.
If you SAVE data that you create (not just the Performances are saved but any user data), highly recommended, your User Files will contain YOUR Utility Settings!

If you load someone else’s .X8U File, please recognize that your Utility Setting will be changed to the preferences of the author of that file.
To avoid this, remember that it is quite normal for your Settings to be stored and restored when you SAVE and LOAD your own Files.

Once you are aware of this, you will no longer rely on the Factory default *Standalone*, you’ll simply *know* to restore your own by simply loading one of your own Files.

EXTRA CREDIT:
If you have an old File, or a file you got from another MODX Owner, that has the original Factory defaults for Utility Settings, you can update that File as follows:
Load the .X8U File — take note of the exact File Name.
Once it loads, review your Utility Settings, making the changes to your current preference
When you have reviewed all settings, tap “Contents” > “Store/Save” > Set “Content Type“ = User File
Tap the File Name
You will receive a warning that you are about to overwrite this file... and since this is exactly what we want to do, proceed.
This will update that User File to include your Utility Settings.

So rather than touching “Standalone”... know to LOAD a USER FILE that you made. All your User Files will have your Utility Settings. Make sense?

Your User Files will contain your Utility Settings (which include the Global MIDI and Audio Settings)
Data that is stored to the dedicated area in the User Memory can be saved to USB flash memory.
Data saved as “User File” is as follows.
• Performance
• Arpeggio
• Motion Sequence
• Curve
• Live Set
• Micro Tuning
• Waveform
• Utility Settings
• Quick Setup

Thanks for the suggestions on how to manage this!

Loading a user file is certainly an option, especially when more changes have been made. But I would like to also be able to use a quick setup preset to quickly get the keyboard back to one configuration or another. That's what this feature is there for, right? It's a bit odd to me that the Standalone preset cannot be overwritten.

So I guess what's left is for me to create my own standalone preset, which would mean getting rid of one of the existing ones. I definitely need the MIDI and audio recording presets, so the one that would have to go is the ARP record one. Is that one the same as MIDI record but with ARP MIDI output enabled? In that case I could just manually enable that if I want to record ARP data.

There you go...!
Make sure you NAME it...