guiser said:

For people who want the burned in sub scenes clean, would it be possible to render just those scenes by themselves sans subtitles as an extra?

They could even be encoded at a slightly higher bit rate since they may be used in other projects and thus re-compressed later.

Or could the files be stored right in another directory in the Blu-ray (only visible if the image is mounted or the disc is viewed as data)? I thought this was possible with DVD, but have never heard of doing it with Blu-ray.