It's not said that they are alternate universes, just that the Dragon world is made up of 12 universes and that there are fighters stronger than Beerus in other universes. One of the guide books (I forget the name, sorry) implies that the universes are all unique and Toriyama himself said-
" Ive written a strange new story where they finally depart from this universe."
and
"Since its another universe, loads of new characters will turn up. Ill do my best to draw the tons of character designs necessary, so Im looking forward to this too."
which to be fair doesn't mean that it won't be an alternate universe, but the way he brought up there being "loads of new characters" makes me feel like each universe is unique.
The only things that point at them possibly being alternate universes is that Champa and Lady Whis look very similar to Beerus and Whis and Universe 6 has its own Dragon Balls. But really we don't know enough about the Gods of Destruction and their handlers for the former to really be any indication of anything and the former could just be explained by Dragon Balls being a thing that are an inevitability in each Universe.
I think the closest we'll get is equivalents to some existing characters, for instance Universe 6 might have an equivalent to Goku, but he's not Goku, he's not a Saiyan, he doesn't really look all that much like Goku and he doesn't have the exact same personality.