So, the new mutate abilty reads :
As a mutating creature spell resolves, instead of entering the battlefield, it merges with its target into one creature. Its controller chooses to put the resolving mutating creature spell on top of its target or underneath it. You'll end up with a pile of cards that all represents a single creature. That creature will have all the characteristics of the top card, and it will also have the abilities of every card underneath.
If my commander is on the top of the pile I'm pretty sure the pile will be my commander (and will be able to deal commander damages) but that happen if it's not on the top?
The closest think I can think of is meld, but I'm not sure it applied to mutate.
903.3bIf a player’s commander is a meld card and it’s melded with the other member of its meld pair, the resulting melded permanent is that player’s commander.