jschaffer, If you add the students who need accommodations into the course with different user rights the best you could do is give them the ability to do things that normal students can do - ex: manage (add/edit/delete assignments and quizzes). This setting can't be used to automatically give them more time or extended due dates.
Applying the settings course by course (and student by student) is the only way I'm aware of to provide different settings for different students. There could be a way to do this programmatically on the back end of Canvas, but for that you'd want to see the assistance of the Canvas Developers group in the Community (they do the back-end programming with Canvas). In addition, you might want to check out this feature idea - - it sounds similar to what you are wanting and is currently under consideration.
Sorry I can't be more help!
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