1 thats not true... threejs can import Fbx without any bones, rotated or otherwise
example: this Mixamo model has had custom hair added then converted to the old [1974] Fbx standard which loads in both Blender or 3js


2 what i recomend is you stop using 3js until you have a solid understanding of json... even then its not a great tool because so few people want to use it
learn Blender first that will give you the basics and works on almost any system then if you need to go pro move onto Iclone which is Windows only & $ but works right out of the box and is much better supported than 3js
3js is a web code based display... thats its strength and weakness
not many people want to learn the code and most clients systems will block web based code because they feel its not safe