Don’t count on epic.
What they are doing so far is just using the existing FBX export.
The problem in everything is the poor conversion of the FBX export compared to it’s native Autodesk version.
If they ever decide to read the .blend file and import from that - then maybe, they’ll be able to offer a more robust solution.
Otherwise complications and limitations will be much the same. What’s more, if you watched the announcement video and how they get things to work, the current setup will destroy 90% of all prior work by requiring you to manually split things into different collections.
You can add BoneBreaker (Bone Breaker: Unreal to Blender) to that list of add-ons.
Working on releasing a quick update to address the Pole change issues as well.
With your own custom rig bone orientation usually won’t matter.
The OP’s issue isn’t really related to that. Though in general, Primary is Y axis, Secondary is X axis. (blender’s armature tab in export). while the orientation of the axis on Main is Y forward Z up.
Again, nothing to do with the OP’s issue really.
You could even try to import the mannequin, delete the armature. create/scale a human meta-rig, and automatically parent the thing - then export.
The imported FBX skeleton will work - just won’t have epic’s nomenclature or hierarchy anymore. Since most of us create stuff that is marketplace compatible we look to solutions that allow to keep that bone structure the same as much as possible…