Unfortunately I don’t have time to answer questions about how to work around Mail-in-a-Box. As a last resort, you can always look at the source code and modify it for whatever you need.
Possibly you could add a file in the /etc/nginx/conf directory with your specific site configuration. That file will not be touched by mail-in-a-box. I say possibly because I’m no expert in nginx configuration and don’t know what that file should look like.
nginx is setup with /etc/nginx/sites-available and /etc/nginx/sites-enabled with the expectation that you would add any site configuration to sites-available and then create a symbolic link pointing to it in sites-enabled.
As far as I can tell miab does not mess with this setup. Any page you setup will work, with one exception: The domain you used while setting up will for some reason be covered on top level by miab. So, no www.mydomain.tld or mydomain.tld for us. Which is a bit weird