Best practice for sharing in bigger organization

Nextcloud version (12.0.2):
Operating system and version (Ubuntu 16.04 LTS):
Apache or nginx version (Apache 2.4.18):
PHP version (7.1):

The issue you are facing:

We have a relatively big organization, with lots of folders and docs. There are several occasions where we need to add edit permissions on sub-sub-sub levels of the structure for some of our users. As I learned from my previous post, Nextcloud by design creates new and new “root” folders for each of the editable directories which makes managing of them a nightmare…

So. eg., we have a folder structure like this:
|_ SF1
|_ SF2
|_ SSF1
|_ SSSF1
|_ SSF2
|_ SF3

If I grant read access to Joe on MF1, there will be an MF1 dir in his share. Cool!
Now, I grant edit access to SSSF1 to him - he will see “MF1 and SSSF1” in his root folder, not too good.
Furthermore if I grant edit access on SSF1, it’ll get even more confusing, given the fact, that if he opens something “via” MF1->SF2->SSF1 he won’t be able to edit it…

So the question is, what is our best bet to not overload their “root” folder, still having the possibility to edit some of the sub folders? Thank you in advance!