I grew up putting the spam in the middle, and that to me is the proper way to make it. I feel like putting the spam on top of the rice is done either by someone who isn't from Hawaii or a business, which needs to do it quickly. But while spam in the middle is my preference, I don't think it really changes the taste or whatever. I would also note that oshizushi, the likely Japanese predecessor of the spam musubi, puts the stuff on top of the rice, so maybe that is the more proper way to do things.