When enrolling users via the LTI provider you should be able to assign them to a group

Hello,

There should be an option that when you use LTI registratrion method on your course you could choose that these users are automatically added to a group of your choosing.

This way you could easily tell apart "core" students from the LTI-students and user f.ex. separate groups option and easily tell them apart on the Moodle reports.