I haven't really been following this thread, but since my run was brought up.
it seems like the most fair way to handle that would be to tally all the deaths and add them to my final time. the significant issue here is that the in-game timer doesn't track seconds, though, so the whole run would probably have to be manually timed which would be a pain in the ass to make it comparable to other runs of the game due to how the in-game timer works (basically, any time you are not in control of Samus, the timer isn't running, so all cutscenes are factored out). I do know that there is something similar used in Metroid Prime 2 though, where the game gives you a checkpoint after beating Emperor Ing but before Dark Samus, so runners intentionally kill themselves so they can try to optimize the Dark Samus fight without having to redo Emperor Ing every time (with DJGrenola's 1:38 run he opted to label this as a separate segment), and with that precedent I'm planning on doing the same thing with the final bosses in my segmented run of MP3. So if we have a precedent that restarting from checkpoints counts as a separate segment, then for SS runs, obviously they shouldn't be labelled segmented because of an unintentional death, but we also don't want runners trying to make deaths look unintentional so they aren't penalized for it, so manually timing runs with deaths looks like the only way to handle this (and more consistent with the way the rest of the games are timed).
Your Mainbar: