I believe "shadow factions" actually only refers to the Roman rebel emergent factions in BI; AFAIK the concept is not used in M2TW. I understand it is a common misconception that it simply means two factions which are programmed to hate each other, or factions whose victory conditions include the other's defeat.

AFAIK any factions can ally with each other in M2TW, I believe the main thing meant to ensure that England and France go to war and do not ally is the fact that they share a land border (I think AI factions are reluctant to ally with people the share borders with).