Alpha Mods are different from Omega Mods. Each individual Alpha mod you purchase can only be used on a single weapon at a time. Unlike Omega mods which can be used on any/all appropriate weapons once purchased.

The good news is that means you can stack Alpha Mods on a given weapon. Put two or three bolt multipliers on the Mega-turrets in the Endzone Challenge at DreadZone station and watch the bolts come pouring in. Similarly, you can pump up the experience Ratchet gains from using a given weapon. Hope that helps.