1. Mods are outside of their control and given what some people have done with mods and the disaster that is the modding discord, can you honestly blame them for not wanting to deal with it?
2. Japan has strict copyright laws and many mods outright rip models from other game franchises - with Black Desert Online being the one that gets stolen from the most. "Well they should just make sure they aren't from other games!" I hear people say, but can you imagine how hard it would be to track down a specific model from a specific game if you've never played said game before? We're talking extensive research for basically no positive return, just to make sure they don't get sued. You also can't trust individual modders to be honest about this either as while many are good people who would turn to creating custom content, many of them are NOT. In-fighting over stolen work - like actual custom work, not taken from an existing IP - in the aforementioned discord isn't uncommon.
3. Quality control. SE would need to test each mod personally to make sure it:
-Meets their quality standards, so no pixelation, the item has proper physics, etc
-Doesn't have broken meshes
-Doesn't cause weird graphical glitches if you're turning just the right way in the right light.
-Actually works for both genders and all races - as mods that only affect one or the other on an item assigned to all races/genders cause fairly bad texture and mesh issues for the gender/races that get left out.
It's a ton of work and unlike Skyrim, FFXIV wasn't built with modding in mind. Skyrim and Fallout both use a modified version of Gamebryo - with the current iteration being known as the Creation Engine. This engine and it's predecessor were designed to make modding and editing easy to accomplish, with Skyrimg and Fallout 4 outright offering a creation kit to modders to go have fun in their own proverbial sandbox. The engine FFXIV uses doesn't have that level of accessibility. It's not as bad as trying to mod, say, Frostbite - which god help you with that since Frosty Tools only /just/ partially cracked it beyond texture/mesh modding - but it's not as easy as you seem to think it is even with the modding tools we now have available.