Nice summary. Unsure about the "fix it later" part, though. I've been the major (sometimes only) contributor to this forum for several years and have witnessed some amazing missteps in the development and release of various versions of Toast. Given the history I know, I'm impressed it works this well. What's needed, though, is something totally new rather than patching and adding on new features.
Yes, the repeat multiplexing and long dead time is normal when preparing a Blu-ray video from a HD MPEG 2 file. You also may experience a crash at the end of writing the Blu-ray disc from a disc image. The disc plays fine, even so.