Amateur modding seems to be better looking than professional in-game options?

[Eloah]

One of the biggest things to understand is that modders aren't constricted by deadlines, budgets, or having to worry about the game's rating/system requirements and going through Q&A testing. It's easy to make stuff look super high quality when it's a single mod you're working on because you enjoy making it, rather than having to make literally an upwards of 100 pieces of gear every 3 months which you may not enjoy the aesthetic of.

In addition, Square has to setup the coding, database entries and many other things that are already pre-established for modders to come in and basically plop something they've made over something existing.

This, pure and simple. I mean it's the classic, "your job isn't so hard, even I can do it" or similarly the "grass is always greener" approach. Just because you perceive something as better or easy, doesn't mean it is.