Re: I'm just hesitant to have to alter those joints and weights after paying someone and them saying
Yea, I get what you are saying but there seems to be a problem with the joint orientation of target skeleton (warped mount). They don't see to coincide with the source skeleton (one with mocap). They might be the same hierarchy but if they don't have the same joint orientation then it will not work.
Do you have the default/neutral pose of both source and target skeleton? That way you can compare it properly.
RE: doing all the work in Maya but he says he tested the animations and they work.
Are the retargeted mocap working for him? Do you have a screencap?
RE: Maya is less strict about exact skeleton hierarchies??
I worked in Maya and C4D. And more or less they have the same nuisance with hierarchy.
For now, just retrieve the default/neutral pose of the mocap skeleton. And I'll take a look at it.