If you received a complete engine and transmission assembly then you started fresh with a completely new engine which includes a new cylinder head, so this would have involved starting fresh. I remember your situation and this would have been the right thing to do ... but for some reason, the motorcycle manufacturers (all of them) are extremely resistant to handing out "crate engines". In the automotive industy, this would be done without even thinking about it.
If they tore down your engine and inventoried every part that needed to be replaced, and only replaced those parts and nothing else (which is probably what happened based on how the motorcycle industry operates) then the cylinder head wouldn't have been replaced - and since checking and resetting valve clearances wasn't involved in repairing the failure, it wouldn't have been done. If someone isn't paying for it to be done then it ain't gonna get done.