We do have a feature in the LMS version that should accommodate the difference in email addresses.
Connecting directly to MathWorks.com websites and logging in will use whatever SSO solution the school has set up, in this case Shibboleth, for accessing MathWorks cloud offerings. That would apply to logging into grader.mathworks.com and would be needed for the LMS Admin to log in there to generate their LTI keys for the MATLAB Grader implementation. This would also impact any instructors that might go to grader.mathworks.com to author content collections, or if they have used the hosted version of MATLAB Grader in the past.
Once the product is implemented in the LMS, the instructors will log in through the LMS, and will use whatever identity management solution the LMS uses. When prompted on the page in the integrated version to link their MathWorks account, the instructor user should use the same email address they use when logging into any other MathWorks.com website directly. Instructions are in documentation here: https://www.mathworks.com/help/matlabgrader/ug/link-mathworks-account-to-access-matlab-grader-coding-problems.html