Well, The only place in ISPConfig where web-service paths and settings are set is under system->server config->web.
Of course there is the "options" tab with every web site you define...
I've never played with ngnix so I can't really say if that is where you'll find something.
Now for Apache, I do make changes to the main config files to suit my needs. ISPConfig does not routinely overwrite those (only with an upgrade I think).
So your approach may be fine, but I'll defer to the more knowledgeable people here.