with what has been said. The odd thing is that from what I read your doc says just to pump and bottle feed, but how would that help? I don't see an issue here, just an issue with an underexperienced doc!
If what he is getting at is the desire to know the exact oz that baby is getting, a more BF friendly thing to do is to rent a hospital grade scale and weigh baby before and after nursing to see how much baby ate.
That said, again, I don't even think the "slow" weight gain is an issue in your case given all the other factors.