You can still use modifiers for abilities.

Basically the automatic FTL is for keys 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, -, and =.
You can copy what the wizard has done, and make any other key an auto assist (via FTL too).

Using modifiers on these keys will probably mess up the FTL.
At least I think it will.
However, I haven't used Shift at all, on my FTL modifiers.
You could easily leave Alt or Control free.
In which case they (well one) could be modifiers for your FTL dps keys.

As far as all the other Keymaps go, if they're not calling the auto FTL, then modifiers don't matter.
If for example, you put Hurricane on Alt + A.
You can set it up so mouse broadcasting applies, until your next click.
It doesn't matter that Alt is an FTL modifier, because you're not using FTL in this keymap.