Because Inno doesn't run a check to see if the same player is in guilds on different worlds before matching them, as far as I know the match is just based on guild size, I'm sure this is on the wiki somewhere but the matching puts all guilds with 70-80 members in the same expedition pool, and 60-70 in another pool, etc, so the only factor in matching up 2 guilds is if they have roughly the same number of players.
The most ethical thing to do is complete the same # of encounters in both guilds. We have had this happen a couple of times, it was not really a problem because 1 person rarely makes the difference in GE scores. It is all percentage based for trophies, so its not 1 player doing 2 or 3 more encounters that matters, it's 10 players who do or don't do 10 encounters that begins to make an impact on the overall %.
Having run a guild for the entire time that Expeditions have been around, it almost never comes down to 1 person who makes the difference for what placing the guild gets in the final trophies. I have checked every time we had very close races if we could blame that 1 person who disappeared or only did 10 encounters, and it was never down to that one person why we lost, if they had been there and done 100% it would not have changed the outcome. In one very rare instance 3 people going unexpectedly missing (doing 0) did make us come in second one time -- that's 1 time in 7 years since trophies began.