The Plague was only designed to be played with the base game, but that doesn't necessarily mean it won't work with other expansions, just that it was not tested with other expansions. I see this as more of an opportunity to experiment and figure out what works and what needs to be tweaked.
Was any expansion tested with any other? The only exception I can think of is the two (?) tiles in River II which use rules from other expansions. The reason behind the CAR is largley the fact that expansions are all just designed to be played with the base game.
The minis from Spielbox -
The people from Spielbox are testing only with the base game of Carcassonne.
expansions from HiG:
The people from HiG (and their playing team) are testing with the base game of Carcassonne and some of the expansions. I don't know if they always play Mega-Carc...
All two years (since 2006) we get a new BigBox with some more clarifications of rules.
published expansions by licence partner like RGG:
The translation of the German rule into English is sometimes not correct...
For example the change of the scoring for the farmers:
- in German the rule changed some years before RGG follows that new rule.