Hey, that sounds horrible limitations in unity. Tho im sure itll be better nowdays.
Anyway, in in ue4 its actually quite flexible. My current characters have rather complex skeletons. around 400-500 bones including twist bones for all limbs, facial bones, and a lot of additional deformation helper joints.
Our skeleton also has different number of spine bones than ue4 skeleton and a different hierarchy setup for spine (No static hip joint) as well as several other differences in orientation, general positioning, naming and parenting of bones. But we still managed to retarget plenty of animations from ue4 mannequin using ue4 retargeting tool, worked rather well. Its not a final solution for advanced rigs as ours - we still have to do the final retargeting in maya to make sure all auxiliary bones move along since they have their setup done in maya.
Regarding twist bones, only important thing is that they arent a chian but rather individual children bones of the main limb bones. Except for that, I havent encountered any hard limits regarding skeletons alone. Theres still some annoying soft limits with the number of bones in a single skinCluster, but thats a different topic.