Hi @simon98
Comparing your *.MEX file with the one for Dio_Example_S32K358, I found something that could be causing the issue.
In your MEX file several update_project_code parameter are equal to false. Let's try the following, open created *.MEX file using text editor and find the XML element for the particular tool that should be enabled/disabled and manually edit the "enable" attribute. For example enabling Pins tool can be done changing from:
<pins name="Pins" version="15.0" enabled="true" update_project_code="false">
to
<pins name="Pins" version="15.0" enabled="true" update_project_code="true">
save *.MEX and re-open the Config Tools configuration.