I am totally agree with you.
In my case i m make a document library for the entire the organisation ( 7 000 users).
For this, i have only 1 level folder
* AURA > only for group AURA -> Modify permission. Hidden for everyone
* BZH > only for groupe BZH -> Modify Permission. Hidden for Everyone
* Commun -> For Everyone -> Modify Permission.
I had to create the folders AURA, BZH because members of the AURA group will drop some confidential document there.
For security reason, i gave the read only permission to everyone to the root of the document library...and i associate the permission "restricted reading" (lecture restreinte in french).
And on the commun folder i gave the permission Modify to everyone

Users use a powerapps form to qualify files with metadata.
Maybe my structure is not a good practice... at first, I was thinking of creating a document library for each folder like a document library for the AURA folder etc... but my company rejected this idea because for them it will be more complex to administer.
If you have good advice to share with me, i will apreciate that.
The flow will allow users to check out their documents in the commun folder if they wish.
Otherwise I found what permission are necessary for a user to start the flow without granting all the Modification permission
.
