I think... if you build the governor's buildings in certain colonial territories (I've noticed it in the US and India), you can't build any other buildings and therefore can only recruit militia; building military governor's buildings means you can recruit a selection of units.
That's only a rough explanation/guess, I'm sure there are some ridiculously complicated hidden rules and variables going on. It is TW, after all...
Maybe looking at the building browser before you do anything will tell you what you get from the alternative buildings. Maybe
(And I think the OP was just comparing the military gov/normal gov building trees with M2TW's castle/city choice)
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