Not that my BP will take a f/t rat regardless of where I hold it, but... Holding it by the back of the neck will make the heat signature look more like a live mouse than the weird vertical posture it'd have being dangled upside down.
You wouldn't think that'd make a huge difference, but I have a couple snakes (non-BP) that have to have food offered held behind the neck. If they can't figure out where the head is supposed to be, they just freak out and refuse to eat.