I talked to an independent mechanic around here when I was looking to get my head done cheaply (ended up sending it to MRieck anyway!) and he clearcoated everything before putting it back together. He was reckless IMO though, he said it was fine on gasket mating surfaces of cases etc.
I decided though, that I'd rather deal with straight dirt and a bit more maintenance of the aluminum than the potential ugliness of a failed clearcoat that requires blasting or stripping to get it off (which would require engine disassembly!!) leaving me in the same place as bare aluminum would.
There are products that help with aluminum maintenance -- I forget what it's called, my vapour blaster sells it.