Argh! I have discovered a terrible, terrible truth (er, at least I think it's the truth...). The Blu-ray format supports only 32 subtitles in PGS format. It supports a few more than that in text format, but there actually is a hard limit either way and it is not merely the bandwidth used by those subtitles. Sorry it took so long to discover this, but it's not very well documented and not many discs even approach that limit.

So, if you want to make a truly universal preservation, it looks like MKV is the format you should use (I still recommend graphical subtitles though). For a Blu-ray, you're going to really have to cut those subtitles down, or make different editions including different sets of languages. Sorry again that I didn't see this earlier... I'll update the Project Threepio README to make sure there's plenty of warning for anyone with such a plan.