Complex hierarchy from Blender to Unity

Hi everyone,

This topic is not the first one on the subject but the ones I have found are <2.8 (and my project is particularly complex).

I started creating a human anatomy atlas in Blender (https://www.z-anatomy.com/) using collections.
A Spanish developer is now creating an app from its content in Unity.

I can of course transform all my collection (the ones that only have one occurance of each object) into groups, parenting their objects to an empty, but it would make the .blend file much less clean (with hundreds of empties and children running everywhere).

The ideal would have been to keep the .blend clean, because it will still be updated regularly.

I have also prepared a great deal of extra collections, with other occurances of the same objects, and I would have liked to be able to recover them in Unity.

For now, it seems that I should convert all my one-occurence-only hierarchy into a great family tree, and keep the extra collection…

If you have a better solution, that does not imply duplicating/forking the .blend; I’d like to hear it.