Rules smell? Of what, stale sweat or blossoming roses?
Of course modified gear affects game balance. If there is no difference between, for example a stock blaster pistol and a heavily modded one, there's something very wrong with how you balance combat encounters. The base stats for a blaster pistol is Damage 6, critical 3, range [medium], 3 HP and Stun Setting quality. Now give that blaster a fully modded actuator chamber (fully modded, for the sake of argument), the Superior attachment and a Multi-Optic sight (also fully modded). Suddenly the base stats become Damage 10, critical 3, range [medium], Pierce 2, Stun Setting, generate one Advantage on hit, remove 2 setback dice for environmental effect, add two skill ranks in Perception and add one setback die to hit. That is an very powerful weapon. A player with that weapon would be significantly better off with it than he would be without it.
Oh, and accusing those who disagree with you of having "underlying problems" simply because they don't share your personal opinions is the lowest form of argument.