I think Phil was already "powered" before Loki killed him. Whatever wild-ass theory you want to apply, Phil Coulson was most likely some sort of latent super and completely unaware of it --- be it alien (Mar-Vell!), robot (LMD!), android (Vision!), biological experiment (Super Serum!), or whatever. He wasn't "just" a top SHIELD agent --- Fury wouldn't have gone through all that trouble. Fury needed to keep Coulson alive, because Coulson was already more than human. I know it pisses some people off who willingly swallowed the Kool-Aid about AOS being about just "normal" people operating in a super-powered world, but the writing has always been on the wall that Coulson (and probably Skye) aren't normal people at all. As for the surgeries themselves, my take on it is that the procedures were a brain transfer. They took Coulson's living brain out of his body before it died, kept it alive, and transferred it to either a clone or an LMD. The "real" Coulson is still alive in a superhuman (of sorts) body.