You want a multisite installation. It has the same plugins for all sites.
Subdomains cost nothing. A single wildcard dns record is all you need. It will be much easier to use subdomains. I’m not sure that the subfolder code is tested in multisite.
Though many settings can be set using environment variables (though they’d be the same for all sites, which is fine for some things like s3 but not others like pop mailboxes) , the best way to apply settings to all sites is probably with a plugin. You can also hide settings from the web interface.
If you have a budget I can help with all of these things.