When you connect PEX with MySQL you can set the Server. so what i mean is if you got multiple server you can set that permission for that group on that server. Like Bugeeperms https://www.spigotmc.org/resources/bungeeperms.25/ (Inactive)
That would be very helpful

In PEX 2 it is possible to set per-server permissions with the server-tags context. The documentation is currently WIP -- currently here, so let me know if that's too confusing and I'll try to expand on it more.