So it is only DTS streams in pre-1999 films that haven't been remastered and re-released since (or you have an old disc)?
I didn't even know that, and certainly don't care if it is removed (I have six DVDs total right now, if I buy them, and I don't, I would rip them and give them away). But, if that is true, and people do have these, maybe a way to do it on a per-file basis would be cool. But, how rare are those discs? How often was DTS used on pre-1999 DVDs, and how many of those have been remastered to fix the problem for newer printings of the discs?
If it is something where someone with a lot of discs they bought over the years, might have 1 in their collection, but they could just re-buy a new copy (or rip it) to fix it, then I'd say don't worry about it and remove it.
But if someone with 200 DVDs from over the years might have 7 or 8 discs that "qualify" (and maybe not even know it), and you couldn't even just re-buy a bunch of them because they've never remastered the audio and the copies they still sell now are still broken. Well then, I think you need some easy way to fix it. But, it seems like the current option would be pretty useless to actually fix those discs anyway, because you'd need to remember which ones they are and make a special Zone to play them back in with that option unchecked.
It seems like the only reasonable way to fix the problem is to have a per-file system, and that the current option is mostly useless either way.