One of the problems that I experienced by using the unofficial folder, is that if required subparts or primitives are not found in the expected relative folders, LDView or POV-Ray will have trouble.
Basically the same as you described.
Your suggestion to let SR3D automatically group sub-models (if not already done by the author), seems also to me the way to go.
At least it is what I also imagined.
The limitations you described about flexible parts are also my concern. Of course SR3D is much easier to work and provides a much "cleaner" approach.
However the limitations to the external renders, are big drawback.
Maybe something for you to work, when you find the time and right mood.
We should have about 10 months, till the next TechREVERSE Challenge...
Of course you are not imposing anyone to use SR3D, but I also agree (from the first challenge) this should be a very good alternative to consider, as MLCad is almost stopped in time and is not providing perspectives of new developments.
LDD is a completely different story!
So, as you already noticed I aim to use one unique proposed tool, also used for the evaluation process. I'm not wooried however, if participants decide to use other tools, as long as they are compatible with the one officially proposed. Otherwise the only affected, is the contestant itself.
TechREVERSE should be also a good way to promote whatever tool we decide to support.
The day you have finished (or almost) all the functionalities you can imagine for SR3D, I think there are opportunities to improve the design and distribution of graphic elements on the UI. But of course this is a minor topic at the moment.
Also the application icon, is not distinctive and appealing enough. You should seek for less detail but a more eye catching logo.
Don't take me wrong. These are just some suggestions of mine.