Basically, take your science fiction and replace the word "science" with "magic".
Its more modern-but with mechs then "science fiction", but yeah. That is what "Punk" means. I think. If he wants a railgun, I am not going to stop him. Magic does allow for some cool things, but in general the technology would be closer to modern day than futuristic. You know, like modern day super soldiers and wizards. ...Alright, maybe "Near future"
And to clarify, they *do* know what electricity is, as they have a functional model of the atom and knowledge of electrons, they just don't have any way to practically use electricity and have no plans to do so, aside from a shock attack or two. No reason to try powering a light with electrons going down a copper wire when you can effectively light a whole city with a few lines.
Alright, would having the level up-bonuses be more powerful work? or do I need to change it still?
Nope, level bonuses are fixed, it would be rather unfair to give you even a single extra skill point just for a module.
Maybe treat it as having an adaptable system? Parts, particularly weapons, could be swapped out for equivalents between missions, maybe salvage of other crafts' systems at reduced effectiveness in the field through some sort of interfacer?
That sounds interesting, and might work.