Some things I've noticed in the SNES version. These may not apply to all versions, and perhaps I am misunderstanding the triggers myself, so take with a grain of salt:

Bret Perot's appearance seems only to spawn if you meet the Piracy Fame threshold AND you've completed at least one battle since the previous story progression trigger. He may only spawn in Mediterranean ports (I've never attempted to trigger him elsewhere)

Ali seems to only appear in a European or Mediterranean port. I've had him appear at around 30K fame, so I'm pretty sure that's correct for his trigger.

The sample text progression I used took 31.26 seconds in US and 16.02 seconds in JP.

After a little testing between SFC JP and SNES US version, it seems that text is almost 2x faster in JP version, so I think JP and US should be recorded as separate categories, since US times will never be as fast as JP.

Typically, I prefer runs to stop time at the last player input required to win, but in this case I can definitely see the importance of having a unified end point for all categories. After giving your suggestions a lot of thought I think I agree with your first suggestion. "xxx day voyage" fully faded-in.

I know some games, (EarthBound, as an example) Have different stop time points depending on if played in English or Japanese. If there is a strong enough argument for that, it could be an option as well.

For now, I've re-timed the currently posted run to end at "xxx day voyage" fully visible.