I have a very similar question I hope Andras or Alex or someone else will know.
We are just now trying to use the LTI authentication (or at any rate, to get grade passback, which I guess requires this?), but not on all courses. I can't find any specific documentation for how to do this, but is this answer the "official" way?
In particular, how does WeBWorK "know" if someone is trying to authenticate in various ways? I just did what you suggest, but now I only get a message like this:
> MAT134-2020SP uses an external authentication system (e.g., Oncourse, CAS, Blackboard, Moodle, Canvas, etc.). Please return to system you used and try again.
And it still doesn't ask me to make an account when I try to get into the course from Canvas, so I am clearly still doing something wrong.