Without any kind of penalty it would so ridiculously overpowered that it would be a must-have feat for all gun builds
Not really. There's been some talk in the past to change Gun Nut to give an additional mod slot instead of the underwhelming damage increase. A good change, if you ask me. It would be mostly on par with other weapon-specific crafting feats, just more versatile. Keep in mind the best mods sometimes conflict with each other (like muzzle brake and compensator or various scopes), so your options would still be limited.
It would probably be the most benefical for ARs. I don't know how meta changed since the smart bonus nerf, but I assume it's muzzle brake and either rapid reloader depending on the frame and caliber, A-A/digital scope or smart module for the few special attacks ARs can have. If we assume someone goes with the brake/rapid reloader, that gives him a choice of additional 35% crit damage, 7% crit chance or +/- 50% more damage on Rapid Fire, Point Shot and such. I could see the crit damage/chance being attractive for crit builds, but it's on par with Bowyer and Weaponsmith. On SMGs it would most likely boil down to 10% precision form laser sight/forward grip instead of scopes. Same for pistols. Decent bonus, but not necessarily worth a feat and possibly investing more points in INT. It would actually be hardly worth the effort for sniper rifles (at least smart, rapid A-A spearheads) since your only options would be an extended magazine and barrel retractor. Extended magazine would give you whole 3 more rounds while barrel retractor is mostly irrelevant now thanks to Strafe.