So there is too ways to fix this problem that is generated with not having upgrading clip/magazine. This seems not fair when using most Automatic Projectile weapons which leaves us with the benchmark of the Rotolaser with the 3rd Battery upgrade since a Rotolaser with the second upgrade matches the Machine-Gun.
1) You Simple allow Magazines to upgrade like Batteries, simple.
2) Can we have a new tech/magic item called Magazine of Endless Ammunition? (Does exactly what it says endless basic ammo)