Hi @mpalframan,
As far as I know MatLAB toolbox does generate FreeMASTER "visible" variables and you would need to manually define them based on the symbolic information from the generated elf file.
To check what symbols are available you need to:
1. Navigate to Project → Options...
2. Under the MAP Files tab select your elf file
3. Press view button to preview all extracted symbols

You can also check this video (@ 2:16) to see how to define a variable based on symbolic information.
Note: I moved this question to MBDT space, so the toolbox team can correct me if I'm wrong.
Regards,
Iulian