It is not going to become an actual part of the federal government, as a new agency, unless Congress makes it an agency. And if they do, then Musk likely would not make the transition to head it as that would involve too many conflicts of interest for him (at least if we still consider laws as things that matter in this country, that is definitely a concept that's quickly being discarded by both the elected leadership and the electorate so you may be right).
Ok, I’m really not sure why the simple answer isn’t getting across here.
His position as co-head of the nominal “department of government efficiency” only exists due to the legitimacy it has been granted by the recognition granted to it by the incoming administration… otherwise we would all be calling it some variety of the first buddy’s pet think tank and arguing over if the incoming administration would even pay attention to it or not… that is a government granted position of power, a position that it is pretty hard to argue is not part of the government that grants it legitimacy… therefore making it a position in government… even if it’s unpaid and advisory… it’s still practically in the government if not legally (for all the conflict of interest reasons you highlight)…
I’m not trying to make a civics or political science case here… I’m talking politics as the exercise of power by government upon the governed… he is currently having breakfast lunch and dinner with the incoming president, making arguments and shaping the cabinet, and contributing to the transition team… he’s involved with government… he’s “in” it.