Hi @ksihota 
Thank you for the answer. We seem to have a similar installation path 
I’ve tried also SNAP at first but wasn’t happy with the result.
I’ve achieved yesterday my third regular (not snap) install attempt and…suprise ! It seems to work…I’m still holding my breath for now thought …but copying files manually (approx. 400 000 files, 2 TB of data, 24 hours of copying) went fine this time…
I’ve not tested yet apps.
Have you tried to add www-data to VH owner group ? This may help somehow as both will share the same permissions.
As you seems to be ahead of me in your installation, maybe you already have some answers to this question too ?