Based on what he told me and about their separate save files of Breath of the Wild. It seems the save data for Switch games is saved on the Switch itself rather than the cartridge. Possibly by cloud or something but I am not sure about that to be honest. The reason being he has a different save file to his brother and can only see his one on his profile. He has to change to his brother's profile to see his save instead of his own one.
Except for the cloud part, you are correct. Data is saved to the system, and the save file you access is based off of the account you're logged on to. That means that even games that would normally only allow for one save file will now, by default, allow multiple.
So considering both that and the fact the Switch is a hybrid console rather than a fully fledged hand held. I thought it might happen because even in households with more than one person that plays Pokemon. They are less likely to have more than one Switch compared to having a 3ds each due to it also being a home console.
Here's the thing. Dual releases has never been about letting more than one person in the same household play the game. They main purpose has been to encourage the player to find someone else with the opposite version and to trade and interact with. Siblings, such as my brother and I, have often been able to take advantage of the system, but they were never the purpose of the dual releases. So multiple save files doesn't really make a difference, as two people playing on the same system can not trade and interact with one another.
For what it is worth, my brother and I are eventually planning on buying a second Switch so that we may both play Pokémon, and other games, at the same time.
And since one copy of the game is needed for multiple people that live in the same location to have their own save file via their profile. I could also see them selling less copies of the same version let alone two different versions. Even in the case where one individual might normally buy both for themselves to play through and then use via Poke bank. Still selling well enough to make a profit but not as many by virtue of how many people own their own private Switch compared to a shared one.
Once again, there may be many people who bought two Pokémon games, but the purpose of the dual release was never to get one person to buy two games.
That and the fact that when the Poke bank is transferred to the Switch you will still have access to all the Pokemon from the previous ds and 3ds games and the cost of Switch games. Being closer to home console triple A titles (at least over here anyway) at about £60 plus at a time. Presumably because those games require more time and resources such as labour to make. I can see it being worth more to GameFreak to make it so you have to trade for Pokemon that become unavailable to you through choices you yourself make in the game. Rather than make two separate versions to get the same result. Since lets be honest there will be trading on-line even if only one version of the game existed.
As PrinceOfFacade said, the dual release really is a marketing device, more than anything else, and it's a marketing device that requires relatively little work from Game Freak to enact. Think about how little effort would actually have to be put in to make the version exclusive features. There really is no reason for them to drop it to save work.
Of course I am probably completely wrong about this. But then again this might just be the time they decide to make each second game a sequel or like the third version instead of a pair.
And to be fair, I suppose it could happen, there's just no real basis to believe that it will.