Hi,
I'm afraid that this is not supported by Advanced Installer. During the build process all the merge modules in the project are used.
However, you can try using multiple builds. A merge module is added to a feature and features can be set per-build. Therefore, you can create a new build in the Media page and use it for the features of the merge modules you want to disable. After the project is configured, you can use only the main build.
Regards,
Cosmin