Actually Turbo, i think you're right regarding units with multiple region bonuses. Only the first region gets the bonus.

In VI, one needs to have at least a castle2 in provinces that start with no improvements for the AI to start building the required buildings to build units with the regional bonus. Otherwise all the AI seems to build is a warrior hold and an abbey?

Therefore the way the current VI is set out with the capitals of each faction being the only provinces starting with improvements, it's best to simply remove all regional unit bonuses. IF you apply them to the capitals (which have buildings already) then the AI will proceed to build the stated units, however, it only seems to hamper the AI from teching up further.