Hello @IsaacHclark
I am not familiar with MATLAB and their LMS integration. However, I know that some integrations do not always get along well with Speedgrader. This might be why you can't view the submissions in Speedgrader. If the submissions are supposed to be visible in Speedgrader, it might have something to do with the LTI Advantage Services settings seen HERE for the MATLAB Integration.
As far as why the option to download submissions isn't an option, this is because Bulk downloads can only be used for file uploads, text entries (displayed as HTML files), website URLs (displayed as HTML files), and Google Docs submissions. Based on the MATLAB's documentation, the tool can only be used as an external Tool Submission type.
I spent some time looking through MATLAB's community HERE and it does not seem like there is a way to hide the results for students, unfortunately.
-Colton