I noticed that religious units (Apostels) can initiate combat against other embarked religious units even when embarked themselves. This means they gained a 20 combat strength advantage when attacking on water. I have no idea why they are able to attack on water in the first place (reciting their holy book verses against each other while on a boat, until someone gives up?), but it is what it is.
So to even this out, they now receive a -20 attacking modifier when embarked, as well as the...
Sink Those Transports! 1.2
Embarked units receive a -20 combat strength modifier