Looks like a good solution, but what happens if an existing containers upgraded can the new containers to access the stuff under root from the non root account ?

Yes, if you reassign owner of files to whatever PUID and GUID values you have set with chown -R...
If obsidian runs as root, all files created with be owned by root. With proposed changes files would be owned by PUID:GUID.

Test it in your system before merging :)