I seem to recall reading that Tracker will be monitoring the user's home directory and removable media, not the entire file system. However, I'm not immediately finding a reference for that when I search.

Regardless, trackerd supports simple directory inclusions and exclusions via its configuration file. Applications that install media files that should not be indexed into locations that otherwise will be, should add appropriate exclusions. Failure to do so will be a bug that should be reported to the application maker. And, should the application maker fail to deliver the necessary fix, I expect it would be a simple matter for someone else to make a tiny deb that adds the exclusion for the average, command line averse user.