As part of this mod there's a couple of other mods that come as dependancies, two of these relate to pistol slots, but they have to be disabled as apparently they're depreciated/part of the base mod now.

My troops all have pistol slots, and I have spare pistols, but all options are greyed out when I try to give them a pistol.

I get the same thing with the Sparks auxilary slot after researching 'mechanized arm transformation gears' in the proving ground. I think this one relates to a different mod specific to Sparks, but still interesting it's the same problem.