Ive mentioned this in my current runs but the swimming mechanic has changed. Possibly due to the grapplebug mechanic change as well. Where you could easily string together fast button presses to swim faster, the new version absolutely denies any fast pressing. This increases the void sea time tremendously!
So I was thinking about it and I believe with any runs that use a passage, a clear .sav file should be used.
This will prevent passages to shelters that you have not been to in previous runs i.e. my 1hr 04min speed run.
Also, I believe doing pilgrimage will be the fastest way to clear the game regardless of passage or not so I think there should be a 5pebbles run as well (passage/no passage).
I'm just spit balling some ideas. Happy running!