In general, reason for this are in Blenders limited interpretation of joints and connections between these… It isn’t an insult but a fact. I’ve tried to iterate this in the past, with weak results… see threads:
Import and export:
And here, on the nature of joint orientation in Blender (see my answers, it got a bit toxic TBH):
It doesn’t help too much… the sad fact is that you’ll have to go through some constraint nightmare on untouched rigs that are suitable for UE.
Infact, I just came across new project, by Jim Kroovy (seems to be a very skilled guy) - he has a new (FREE!) project called “Mr Mannequins Tools”. I don’t think he has a thread here in Blender Artists.
Just do google and see his Youtube videos and Reddit discussions. He talks about the same issues - why export / import to/from Blender doesn’t work properly. It might not be exactly what you are looking for, as he has done complete pipeline for mannequin only, but he iterates the core issues that cause the headaches. You get some good info and hopefully can dodge some issues you have now…
Edit: This sounds interesting, quoting Jim Kroovy, from his UE forum thread: "i’ve started work on a script to make any Blender built armature compatible with my export script " and seems like he has already shared this export code with his Patreon Patrons.