The fact you can do that is just another weird quirk resulting from Salamanders not being missiles in some ways and being missiles in others. A weird and unintuitive fast missile rack interaction is hardly a good reason to keep them that way.
You've got a point. There are 3 mechanically different weapon sub-types within missile group.
Clip-based Pilums.
Reload-based Salamanders.
And finite everything else.
Maybe Extended Racks should affect all 3 but in different ways? Faster reload for salamanders and combination of faster reload and stored amount for pilums. Of course these stats are boosted only by lesser value, for example 25%. Not 100% that finite missiles get to their capacity.
Also, the Mudskipper MK2 needs the Paragon's targeting supercomputer to make it viable as a defenseless artillery piece
It's a joke ship/large weapon pinata. I don't think making truly viable was ever intended.
Plus it's immersion breaking proposal, where would a trash ship modified by pirates get state-of-art targeting system?
Doesn't mean it wouldn't make the game more fun by adding another ship to the player's arsenal that fulfills a role no other ship does.
Also, the pirates wouldn't have gotten a state-of-the-art targeting system, they found a LPC for one that auto-factured one that's barely compatible with an extremely modified Mudskipper whose entire frigate freighter cargo bay was gutted and reworked to look, to the computer, like a paragon's processing bank housing center
Mudskipper mk 1 doesn't have much of a cargo bay in the first place (and is not diminished for mk2...). If 70 is enough to fit ITC, I'd gladly gut any DE and above to do the same. As would any competent military force. I'd rather not want starsector world be populated only by combination of ingenious pirates and bumbling fools in all other factions.
Gameplay-wise Mudskipper mk 2 that is not a joke approaches dangerously close to ultimate kiter archetype for something so ubiquitous. Speed + range + hard flux. And it can double vent rate for no cost, since there is only 1 weapon anyway. It's not that expensive to restore to remove Ill-Advised modifications either.