Yes Mot is not vattable!!!
As for mark up on parts it's up to the garage themselves but check they are vat registered as they shouldn't charge it on labour otherwise and as said only the vat on part prices PAID should be added.
Id say if their a Mot centre doing repairs theyd almost certainly be vat registered.
Makes a big difference to the old bill 20%,people always used to turn up at my place trying to get the vat knocked off,it's not always worth it from a business owners point of view.