Perian works with any QuickTime player, so if the one that Apple makes is inadequate for your needs (on this you will get a great deal of agreement), use a different one. Apple's player only recognizes a limited subset of subtitle types, a subset which is incapable of rendering all the subtitles that Perian can use, so we are forced to use a technique that Apple's player doesn't recognized as subtitles, but rather as a separate video track. Among Apple's players, the only one that allows enabling or disabling of video tracks is QuickTime Player 7, when one has the "Pro" version.
As stated numerous times, this functionality is outside the purview of a file importer. That's why the bug is invalid, because it's well outside the design scope Perian. For this very reason, we've recommended using Nice Player for several years now. It is a QuickTime-based player, and it presents the option of enabling or disabling tracks to the user in its UI.
- Graham