Hi @kmm14,
You may want to talk to your local Canvas admin team (usually in the eLearning / IT / Digital Education areas) about making course sections to differentiate the students. This may or may not be possible based on various factors, like how your Canvas permissions are granted, how users are enrolled, how grades pass back to other systems, etc). If it does end up being possible, you could have one section for point-graded students and another for mastery ones. You could then assign assignments to the appropriate sections. You could even filter gradebook views to only show one section or the other (but you'll repeatedly need to keep switching them around as you change between the gradebooks, or just leave things unfiltered and se all students in each gradebook view).
I hope this info helps a bit! Definitely let us know how everything works out for you as it could be useful to others in the future.
-Chris