Hello Daniel,
I confirm the issue for M1/M2. This will be fixed in a Config Tools v15 update. The workaround (may be for other users as you've already installed x86 version) is to open created *.MEX file (inside the Eclipse project) 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 Peripherals tool can be done changing from:
<periphs name="Peripherals" version="14.0" enabled="false" update_project_code="true">
to
<periphs name="Peripherals" version="14.0" enabled="true" update_project_code="true">
save *.MEX and re-open the Config Tools configuration.
Regards,
Libor