I would prefer it if you left them separate. Just because an alien laser is '20cm/C4 Near UV' doesn't mean it's the same as a native '20cm/C4 Near UV' laser. Russian 7.62mm rounds are not the same size (and not compatible with) 7.62mm NATO rounds. Royal Navy 12" battleship guns were commonly manufactured in 'left' and 'right' versions, and you couldn't put a pair of 'rights' into the same turret.
Captured alien weapons, are, well, alien. They're made for an odd number of fingers, arms the length of an orangutan, and labelled entirely in black text, on a black background, that lights up a black light with a black message when you press the black button. Your empire's copies are modified so that your empire's inhabitants can use them.
If people want X and Y to be that same, they can use SM mode to delete the alien versions and replace them with an equal number of native components. If a lot of people want it, you can add a button to do it automatically. I, for one, like my historical oddities such as the Panzer I Breda, or the Marder - native chassis armed with captured guns.