As EE just sets up the environment so us Admins dont have to slog through a manual process, and the source is available as a GIT, you can go through the scripts and modify them and change the target locations.
If you haven’t used ISPConfig before, it create a client group on the system per user you add, and a web user per site, locking things down to that level. I assume the quota system it has is bound to that client group. The directory structure would be /var/www/clients/client4/web17/web. I would start by adding in those two extra args to the EE script, client4, web17 for example, then change the location that it downloads wordpress to that location. As ISPConfig saves and creates the nginx config from the database, you could hook into that and add the config into the extras portion, the same way EE recommends it.
Lastly, you need to ensure that the NGINX you install has the same components that EE uses. So very doable, but your making a custom solution for your setup, and would need to track any changes EE does to its master version so as to stay in sync.
It would probably be easier to change EE to accept args to have a similar setup with client/web so you can hook the quota system into, a small DB that keeps and tracks these values, and CLI when you change them.