I don't think it would be difficult at all for the subset of people wanting to convert the video to just select the file they want from a batch torrent (if they're converting a complex video from one file format to another, they should be smart enough to understand an instruction on how to download just what they need), and I agree the torrent would probably seed much better as a whole (you can also count that someone converting from a format they don't want will likely not keep the unwanted file and therefore not contribute to seeding said torrent anyway); but, Harmy has his reasons in his head and if he's happier making it easier on those who probably won't seed the torrent, then I won't argue with him, he's got enough to deal with in making these great film recreations as it is.
Actually, one solution that might fulfill both sides of this is if the m2ts torrent puts the file in the same directory structure as it would be in a usable Blu-ray structure, so if you download both to the same parent directory it is usable as a Blu-ray without having to move anything (unless the folders try to overwrite each other in some odd way...), but if someone downloads just the movie, they don't waste the extra bandwidth (just have to go down a few directories and grab the really hard to miss gigantic files). Not that this is at all better than one torrent, but it is a fun way to do the same thing in a far more complicated fashion.
In the end, someone would probably just make a complete torrent that everyone will jump over to and seed instead, if people feel that works better for them. So, if one way or the other turns out to be better than whatever Harmy decides to do, things will course correct on their own eventually, no biggie.