1.can you add support for adding/removing multiple permission nodes in one command please?
[outdated and defunct groupmanager can do this, why not pex? o.O]

separate multiple permissions with a space or comma?
-when removing, ignore perms the user doesn't already have.

Q: can you add a test so when adding permissions you have to have a 'dot' in the permissions node?

ie: 'testnode' is not a valid permission node in any plugin (as far as i know)m but 'test.node' would be valid.
can this be checked before adding permission nodes? (would help prevent accidentally adding groups as permissions by accident, for example)

The permissions would need to be separated by commas, because the next argument after the space is used for adding a permission in a specific world: /pex user <user> add permission world
This comma-separated idea could also be applied to adding multiple worlds for a permission in one command: /pex user <user> add permission,permission2 world,world2

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.