As explained in my other issue (#2464)...

It would be awesome if you could add a feature to the config.yml that allows PEX to save all user groups - even if the person is in the group chosen as default. This exampled is a very handy feature on Prison servers.

Ok, I've pushed a commit that adds this option. Test it using the build at https://minions.aoeu.xyz/zml/pex-1.23.5-dev-savedefgroup.jar and let me know how it works.

So far it seems to work quite well. Still testing though... Will let you know if anything is wrong.

Unfortunately PermissionsEx is currently unmaintained and no further updates are planned. Because of this, all pull requests are being closed. If you are looking for an actively maintained permissions plugin, take a look at LuckPerms. It is compatible with major server platforms and can import data from PEX.