IS Boxer has added an Addon for you. This addon has the FTL stuff in it, along with other macros made within IS Boxer, and does these for you in the background.

There are three mapped keys, which use the FTL stuff. Everything else which depends on FTL references one of these:
a) FTL Target Me
b) FTL Follow Me
c) FTL Assist Me

If you were to disable the IS Boxer addon, for a given character (or for all characters) then the FTL stuff (along with macros made in IS Boxer) would cease working. Straight keybinds should still work, and warcraft macros on those keybinds.