I don't really see how that's really a problem in the examples you listed. If the in-film subtitles are burned in to the film, and the foreign-translated subtitles for non-native viewers are generated in the matte... boom! You have everything.

Also, even if it was a piece of media that didn't have a matte (was the same ratio as the television), it's really not that hard to read subtitles over subtitles. I've had several experiences like that with foreign language media, and it's never been a problem.

I also disagree with your sentiment that home video shouldn't strive to be as close to the theatrical experience as possible. I mean, hell, isn't that part of the reason this site exists?

ALSO... just saw a clip from The Director's Edition, and the subtitles appear perfectly fine there. Certainly not some player-generated, pixellated crap.