Exactly, it took me a bit to figure this out too. You can MAKE a button be a modifier, but then that is its only function.
The up-side of this is you can make any button a shift key (some sims would only let you use the shift, ctrl, alt and that was that). With my old (but still very servicable) X45 I now have every single HOTAS key assigned to a button or hat and it truly does make all the difference when actually trying to employ ordnance.
I was trying to explain all the steps to lock up a target with the targeting pod using the default keyboard commands and it's about impossible.
I made a cheat sheet to keep track of what all the "*MS" switches do in each SOI mode that helped me a ton in the beginning too: