I'm using PEX groups instead of the built-in group system in this plugin. Would it be possible to listen for users changing groups in PEX / Vault and automatically refresh the nametags?

We listen to PEX's PermissionEntityEvent which should automatically hook in, and accomplish what you're asking for.

https://github.com/sgtcaze/NametagEdit/blob/master/src/main/java/com/nametagedit/plugin/hooks/HookPermissionsEX.java

I was using v4.0 (from spigot). Updated to the newest development build and it automatically refreshes just fine! thanks. :)