It does matter.
You specify user roles for the entire application. You then map the userrole to each relevant module role in the project security settings. If you only have 1 'administrator' module role in the administration module and both the MxAdmin userrole and your secondary admin userrole both have administrator rights in the administration module, they will have the same access rights (withinin that module)
Don't ask me why or how, but I've redownloaded my model from the teamserver (because my modeler crashed and corrupted something) and now everything works as I intended...
Case closed! Thanks for the help anyway.
It seems like this issue was fixed in the 7.18.0 release.
Quoting the 7.18.0 release notes: "We fixed the issue causing the built-in admin user to retain old roles when a new role was selected in the Security configuration of the app project. (Ticket 65664)"
First thought that comes to mind is checking the module rules for MxAdmin and the custom admin. Did you seperate the security in the concerning modules?