He hasn't broken with anyone. He's made it clear that if and when any policy changes regarding transgender sailors are handed down by the Secretary of Defense then he will carry out those changes to the best of his ability.
The ball is in the President's court. No instructions have been given to the Defense Department concerning transgender. A tweet isn't sufficient. If the President is serious about banning transgender then he needs to give the Secretary of Defense a formal policy to follow.
I agree with you. The SecNav is correct. The current policy regarding transgender service personal stands until President Trump gives an order to SecDoD changing that policy. Tweets don’t count.