gamefreak does consider them new pokemon but not new pokemon.
Any time they've showed off new pokemon together, megas & alolans are usually lumped in where applicable. In gen 4 especially, Shaymin & Rotom's forms used similar "new pokemon" language in their lead up iirc.
The most notable image I remember is during the gen 6 prerelease, where they were going over all the pokemon revealed up to Honedge and Mega Mewtwo was there (marked as ??????). Mega Mewtwo in general was, before hte mega revealed treated as "a mysterious pokemon with a connection to mewtwo" which was utterly hialrious because we literally saw mewtwo transform into it.
It's bizarre thing in general.
Yes, I remember the Mewtwo thing.
If you add the number of new Pokemon to the number of Mega Evolutions in generation 6, then the sum should be in the hundreds (I think). By that logic, they actually did make more than a hundred new Pokemon. How many gen 7 and Alola forms are there combined? It's probably over a hundred too.