This used to drive me absolutely nuts :? After some time I came to notice a rule of thumb that may be useful:
Mate and align get faces together. The question is where the rest of the body will lay. Lets think of two soda cans.
:arrow: Use mate when you want one can on top of another, like if you were making a tower. In this case, two faces will be touching each other but the rest of their corresponding bodies will be facing opposite directions.
:arrow: Use align when you want both cans to still have a face touching each other (or at least belong to the same plane), but the rest of their cylinders to be facing the same way, as they would be on a six pack.
Happy thing is that if you get it wrong and your bodies flip, you may just edit the contrain to make everything right (you do not have to kill the contrain, rotate the bodies back to original and reconstrain).