I guess that's true. I'm trying to remember if I've ever seen a track with only a handful of subs that wasn't supposed to be forced. Can't think of one.
I use ClownBD and it has to extract all the subs anyway. Once it does that, I look through them with BDSup2Sub for two reasons: (1) move subs into the picture area; (2) identify any forced subs. Once I do that, I edit the meta file (if necessary) and let ClownBD continue on its way, remuxing everything back together.
So, this takes time, for sure, but no more than it would take to view the movie in PowerDVD or the like, which I don't own anyway.