wow, really huge! good that RPGs are evolving :)

Xbox version did great if you consider userbase, and Switch version did well, considering that it was released 4.5 years later

Im really surprised about theese X1 Numbers it did really well on the X1 if you the userbase between X1 and ps4.

Did you forget about exclusive Pokemons in each version?
And different sprites too?
There are also a couple of minor changes such different Pokedex entries, different Pokemon locations (as you mentioned) and redesign/layout changes of a couple of locations.
Pokemon was created so people are enticed to buy more than one edition. I own Blue, Red and Yellow (and Green too if it was released in the West). Do you think I would've bought them if it was the same game?

And then you compare it to The Witcher 3 which is identical to the GOTY edition once you buy every DLC. Green, Blue, Red and Yellow will never be identical.

I couldn't care less if Nintendo count them together and others follow suit. Since the very first pokemon Nintendo very greedly made it 2 or more versions per gen at the same time (and nope the GOTY editions sell over a year after and most add few sales and in just DLC preloaded). Nintendo intention was always to have people buy 2 versions in the same household, even more with the very bad single save practice so no sharing.

Modified sprites eh?  Witcher 3 on Switch has completely reworked visuals. Should we not count that?  The visual differences are far more apparent than the differences between Blue and Green. And I think the only actual layout changes are in Cerulean Cave.  

Pokemon was created to entice people to trade with people who had a different version of the game.  That was a huge focus of the marketing campaign.  Some people buy multiple versions of the same game.  Someone a few posts above pointed out that they bought multiple versions of Witcher 3.  And I know a lot of people bought the Witcher 3 on Switch for portability.  The fact that people may want to buy two different versions of a game doesn't really make a difference.  I actually bought Spider-man twice because it was cheaper than getting the DLC separate.  That's counted as two sales for what I'm sure we'd agree is the same game.

And of course, I'm sure there are plenty of people who did not buy Pokemon Red because they already had Pokemon Blue.  I would guess there are more people who only buy one version than people who buy both.  

Special Pikachu edition is substantially the same game with added content.  Which is what the Witcher 3 GOTY edition is.  The fact that people had to buy the game again to access the added features definitely helps Pokeomon's sales, but that's just a function of the technology of the time. But the fact remains we have two separate SKU's featuring essentially the same game with added content.  Suppose that DLC were not a thing and the only way to get that added content for Witcher 3 was the GOTY edition.  Would you then argue that GOTY was a new game and should be counted separatetely?

More to the point though, when should we consider two separate SKUs to be two separate games?  When the content is 99% the same I'd say it makes sense to count them as the same game.  If I was trying to argue that Nintendo had the most 80+ metacritic games last year, and counted Sword and Shield separately, I'm sure nobody would be buying that.