I know you’ve done quite a bit of analysis of some of these flags in commercial discs, Valeyard, but it turns out to be quite simple to set up seamless branching with the right software.
You can do the same yourself. I looked at Blade Runner, Alien 3, T2 Skynet, and they all look identical. And you can compare to even more discs with the menus - they always start with “1” for the c value of the first entry and then “5” for all other entries, no exceptions, & “In Time” is always 11.650 seconds (branching is done in the same way to seamlessly looping menus). Changing those settings in BDEdit shouldn’t be difficult or cause any problems for the disc.