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!