I know this question has been raised here in different versions a couple of times but how does it sound to play the Game 1 with 6 players and then continue the campaign with 4, since probably we won't get hold of 6 people again?
Is it better idea to skip playing it with 6 players and start campaign with 4 players some other time?
I suspect that starting with 6 then dropping to 4 will end up being virtually the same as playing 4 all the way through. You might end up with a couple more buildings heading into game 2 than you would have with only 4 players (or even 4 players and 2 automa), depending on how aggressively the players build.
The big question will be do you (a) reserve those player positions in the hopes that they play again, or (b) switch those charters to inactive, and add their cards to the advancement deck. I suspect that (a) might lead to problems if the players don't come back, due to buildings being out of circulation.