There are 7 possible mods, and all weapon mods have 3 levels - basic (no prefix), advanced, and superior. Bonuses listed as x/y/z correspond to those 3 levels.
- Stock - 1/2/3 Guaranteed damage on a miss.
- Auto-Loader - 1/2/3 Free Reloads per mission. (Reloading doesn't cost an action)
- Extended Magazine - 1/2/3 extra ammunition before reloading.
- Repeater - 5/10/15 percent chance to instantly kill an enemy, regardless of remaining health. ("Executed" text will pop up when this triggers)
- Scope - 5/10/15 Aim bonus when using the upgraded weapon. 10/15/20 Aim bonus when using the upgraded weapon against targets not in cover. (Does not apply to secondaries)
- Laser Sight - 5/10/15 Crit chance when using the upgraded weapon. (Does not apply to secondaries)
- Hair trigger - 5/10/15 percent chance for each shot to not use an action.
EMP Grenades/Bombs
So I just learned from Are Gatekeepers vulnerable to EMP Bombs? that Gatekeepers can actually be heavily damaged from EMP grenades/bombs, and can even have a chance to be stunned by them for 2 turns!
I tested and confirmed this myself. In the following screenshot, I used an EMP Bomb on an undamaged Gatekeeper, and it took something like 12 damage, and was also stunned:
Which is weird, because you can't hack a Gatekeeper, so who knew it had robotic components that could be damaged by an EMP?
Flashbangs
I've heard that Flashbangs (or being disoriented) can lower a target's Will stat, which would make it more vulnerable to mind control. I decided to test this out too.
The following is the Will stat of an undamaged Gatekeeper versus a fully upgraded (i.e. has all abilities and fully upgraded Alien Psi Amplifier) Psi Operative using Dominate:
The target's Will is 110%, which reduces my chance to Dominate to 80%. After hitting the Gatekeeper with an EMP Bomb, followed by a Flashbang (so that it's also Disoriented), I checked the chances again, and the Gatekeeper's Will was still 110%.
I've also heard that Flashbangs (and being disoriented) can disable some of the Gatekeeper's abilities, but I haven't tested this out yet, and I'm not sure which abilities exactly would be disabled.
Best Answer
No, it does not give additional upgrade slots to the Chosen weapons (I verified this in game by doing the breakthrough and then attempting to upgrade, but it still says "Current primary weapon cannot be upgraded")