This is also a big issue for me as well. I've had to start using PDF because of the disparate methods of formatting supports across various sites, and the inability to simply upload as PDF is a big barrier to my being able to effectively utilize FurryNetwork.
FurAffinity only supports BBCode in plain text, rtf, doc, docx, and pdf for their stories
SoFurry has a buggy-at-best text entry box that, if I have to manually copypasta to it, completely eats all of my line breaks and formatting
InkBunny comes close in supporting doc, rtf, and txt with bbcode formatting, but no PDF support.
I don't know anything about Weasyl, mainly because of the complicated and obtuse content rating system as well as the attitudes of the admins on that site, so I've kept it at arm's length.
Really quite a nuisance that there's no consistency for writers. :\ I feel like FurryNetwork is really missing out on a huge opportunity to gain a LOT of prose artists by restricting story uploads to a Markdown-formatted text entry box.
[Edited slightly for more detail where I forgot on the original posting]
Customer support service by UserEcho