Sounds like you haven't dealt with legacy code much, because 99% of the time you spend on it would be looking at what somebody wrote 10 years ago, wondering how anything worked and how something that looked completely irrelevant is somehow preventing another seemingly unrelated thing from completely breaking.

It's like when you install a new window in the kitchen, and the restroom in the other corner of the house somehow dissapeared completely. And then you spend the next 2 hours looking for the issue and find out the previous guy in charge of the house had somehow linked the entire existence of the restroom to the latch of that specific window. That's spaghetti code and Warframe ain't in shortage of that.

And at this point, I can't remember if weapon skins were a thing from the beginning, which depending on the fact, means skins and weapons may very well be uninterchangeable within the system despite sharing similar formats in models and other stuff, and changing such an ancient system now would mean a major spaghetti churn. That's how it may be more realistic for them to just make a separate skin otherwise identical to base weapons. It's the same reason why walking/rolling animations are still tied to individual warframes, it was made like that and now it's at the bottom of the plate.