The purpose of "Marley-Threepwood" is because of Elaine's notoriety. She has a long standing term as "Gov. Marley". Changing her surname to "Threepwood" or even "Threepwood-Marley" would detract from that. Keeping it as "Marley-Threepwood" keeps the Gov./Marley association. The reason Guybrush changed his surname is obvious as the same reason any couple changes their surnames to be the same at the time they are wed. It's a symbol of unity, that the two persons are actually now one married couple. It wouldn't make sense therefore for them to use different variations of the same surname combination.
Arguably from a "fan's" point-of-view, the Guybrush/Threepwood association is much more important as he's the main character of all the games. But as you said, it doesn't
really matter.
Joke or not seeing as it was in EFMI it should still be counted as official cannon. If it was a joke then it should just be considered as a recurring joke™.