That's easy enough to fix with a single ruling, and one which would prevent a lot of the more insane combinations I've come up with: A weapon may only have one slotless addition added on it. It basically just adds one more slot to weapons, then clarifies what slot a lot of the weapons with no slot text go into.
Edit: And the above creates problems with certain items in Run and Gun, specifically weapon commlinks and weapon personalities.
I really am not seeing any way to solve this easily and have it make sense without either adding more slots, such as a grip slot for personalized grips and gecko grips, or tossing out the entire slot system and rewriting the weapon modification rules from scratch.
Edit 2: To clarify why I say the above...
Run and Gun has already introduced slot double-stacking. Weapon commlink and weapon personality are slotless items, and the gecko grip only uses up a slot on weapons with a stock slot. Problem: It's rules-legal for a weapon to have all three of these, meaning a pistol can have three items that, by RAW, take up the same space and still have room for further modification. Add in Tracker for four items in that slot, and personalized grips would make five. An internal smartgun system potentially makes six (under RAW, it is slotless). Then you can further modify it with a gas-vent 3 (because, at this point, why not?), improved rangefinder, and maybe a laser system just for giggles.
A certain amount of double-stacking is probably unavoidable. But the way it works now? I haven't even maxed out how much can be put in a pistol.