I say BS.
Do you know how much time it takes to get everything out of the Top case/Unibody to actually replace it with a new battery, it will take hours.
You even have to get the display of.
My guess is that the battery is glued with hot glue, they will simply heat it up to lets say 60-70 degrees celsius and will remove the battery and glue in a new one.
If they have to replace the whole top case they would have to do way to much work, if they just replace it with all things inside the serial number would also be different since it is embedded in the motherboard.
They could discharge the battery first(to a hard 0%), Lithium Ion still holds a certain charge even when the computer says it's 0%, it gets cut of below a certain threshold/voltage (3.3 Volt) because if Lithium Ion goes below that threshold it will be broken.
Also the top case/unibody is made of aluminium and too expensive to just replace.
Well your BS call would be wrong. Take it from someone who knows this is going to be what happens. FYI taking everything out of a top case and replacing it takes about 30 mins on the non retina MBP or about 15mins on a 13in MBA.
The battery is glued to the top case, NOT the logic board.
The battery and top case are to be replaced together. Logic board is completely separate.
For those saying the just peel off the battery.. Thats incorrect. I imagine that Apple would require them to be replaced together. Apple authorized technician (Geniuses included) would replace the battery with the top case. Apple's support site states that the battery should not attempt to be removed (separated) from the top case. Safety concerns as you can imagine. The batteries can spark and catch fire if bent. The defective part (top case/battery) is then returned, and they probably have a fancy machine that separates them w/o causing damage. Also, its not glued it, but held in with double sided 3M sticky tape.
Just wanted to chime in and say that all of your assumptions are correct. The batteries in these machines are amazing for what they do, but at the same time you should be very careful when handling them as any damage to the battery cells could be quite harmful to both the person and machine.