What you are calling a firmware mod is a simple parameter change. Two aspects:
- Setting the E-steps is two gcode commands. BondTech provides a gcode file that does this by "printing" it to the printer.
- The only other thing involved is the speed of the fast retraction when you use Change Filament. However, you don't need to do anything, because you will be changing filament using the release lever on the BondTech, and simply pulling the filament out - much faster than the filament retraction.
So do not do anything about this.
As to concerns about changing the original firmware, I can't imagine ever using it again. TinkerGnome's version is so much superior it makes the original seem a toy.
BTW, switching back to original takes one command in Cura and 15 seconds to reload, if you are concerned.