Apologies if this has been posted before, but the bus we see leaving the Phuket terminal is NOT Liz and Marie's bus, but some other random public bus to Hat Yai further South.
I'm surprised the Laurence & Zac got tripped up by the first class issue. While 'first class' is clearly defined in air travel, bus companies in places like South-East Asia can basically call their bus whatever class they like, such as 'first class', 'premier', 'executive' or anything else that sounds important.
As for how the buses could have been reshuffled so dramatically in going to Bangkok, they will have stopped at least 2 or 3 times en route for a 'rest stop', probably at completely different places for each company. Sometimes these can be a quick toilet break, or sometimes even for close to an hour. Speaking from experience, the arrival times that you get quoted for the journeys usually have absolutely no relevance, so it would have been near impossible to work out which bus was supposed to arrive first.