During team configuration, you assign a unique FTL modifier to each toon.
This is done by checking boxes.

The default is fine, I misunderstood the process when I set my teams up.
The FTL modifiers are pretty much only affecting certain keys.
I am free to include shift, alt and ctrl in my macros, without messing with my FTL.
The only thing is, to not use a few hotkeys that the FTL uses, as hotkeys for macros.

Nothing in the default wow bindings conflicts with the default IS Boxer bindings.