Hi Barend,
Since I write in a forum, I will always answer in a way that people with similar questions have use of my reply, so I always go a little bit more into detail. If possible, I have first-hand experience with it; otherwise, I mark it as brainstorming so it is clear that it needs tests.
Yes, I have not seen any Mocap in the past two+ decades that didn't need cleanup. Hence that was the main idea of Kaydara's FilmBox (Filmbox, hence FBX), which later became Motion Builder. A good average is 80% toward usable results, regardless of the system.
Yes, things might improve with tons of IR cameras, but those systems cost $100K and up. There I have only experience with it from way too long ago. Not valuable anymore.
With Rokoko, the best idea is to calibrate often, based on the motion you capture, perhaps per "take", if it goes wild. They constantly improve their system, and it is a sure thing to ensure running a newer version. Of course, as usual, early adaptors might get bitten. If you use Rokoko, take their offer with the one-hour hands-on instruction; it is a considerable value. Yes, I'm a fanboy here.
A good, even while old, book is MoCap For Artists, Focal Press. As usual, every source can hold a gem for you or steal your time based on your already-knowledge.
I would keep the Null Parent zero for P and R (S to one) and no animation. Also, while not knowing your setup, keep the Character object/Skin out of any animated parent Null. You might get double movements at one point.
In the Motion Clips, you can use a Pivot for that. Also, I keep the Character object away from the joints. You can decide how it is connected; see the image. They can live under a main Null, but there should be no mixing of information and definitely no distributed animation outside the weighting. In some cases we had here on Cineversity in the past 17+ years, it showed double movement. Not fun.
But you know better what you need, as you wrote, not a usual project. So I leave it here as a note, and you decide what fits your project anyway.
My best wishes for your project.
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