This is a known issue and I will need to update the description of this mod to reflect that. The only way to get the 33% bonus to mission speed effect is by hijacking the vanilla perk, which in turn hijacks it for anyone else who uses it.

Regarding IMP creation - any new quirks or new specs I add to my mercs will be selectable as an IMP specialization due to the fact that they are "quirks" and not personally assigned unique perks. This is just how the game handles quirks, and actually adds more diversity to your IMP builds. So far I have added:

Enchanced (B.A.T.S.)
Pugilist (Sgt. Slaughter)
Saboteur (Firefly, although its pointless currently)
more to come...

Brainiac shouldn't be an option to select from during IMP creation though, since it's a perk and not a spec/quirk/personality. I couldn't replicate this.

Hi Baja Resident, I started a new run with all your GI Joe Mercs (all great!) but I noticed a compatibility bug: Brainiac talent can be selected during IMP Merc creation and several mercs also have this talent now: Wolf, Jack "Doc" Sheperd from Lost Mercs (by boardmad), Dora "the explorer" Rodriguez (by Smight), also Sonja Cooper and Nikita Korolyov from Varangian Guard mod.