That it was made to be a Mario game from the start is something a lot of people don't know, so they attribute the differences in the game to Doki Doki Panic, when in actuality Nintendo had intended for the game to be a different kind of Mario game. It is technically a Mario game to a large degree. It's different from your example of Captain Toad, because that was just a concept idea that they had several years ago. A concept idea is like a rough draft. It's purpose is just to be interesting enough for the developers to feel like they can build enough good ideas from it to make a good game. But that concept idea never left that stage. At least not for many years. There are many concepts that never get used because they don't fit the game they're intended for, or they're just not a good idea at all, or they end up being used for another game later on, etc.

But Mario 2 was different. It was not just a concept. It was an actual game that was in development where they had already developed several gamplay systems from the original concept, because they decided to make the next Mario game to play like that. And the reason that changed wasn't because it didn't suit their vision of the next Mario game, but because changing the characters from Mario characters into Doki Doki characters for a game that was already ways into development was cheaper than to start over from scratch on a separate game. We can see that this affected the budget of Japan's version of Mario 2, as that game hardly had any inovations at all.
The reason the original Captain Toad concept was laying around for years unused was because they didn't think it was a proper idea for Zelda. This happens all the time. There are even concepts that go into development, and then change into different games because it didn't suit the original game. That would be a closer example to Mario 2. However, the decision to change Mario 2 into Doki Doki wasn't that they were disatisfied with the game engine, but simply because of a business deal and a chance to earn more money. Part of the reason it got reskinned back into Super Mario for the west was because it was originally a Mario game with a system they felt suited the Mario series. And that's something you'd be hard pressed to find any other examples of.
At the same time as Mario 2 was being developed to quite different from its predecessor, so was the sequel to Zelda. If they had reskinned and renamed Link, Zelda, etc, in that game, people wouldn't have noticed that it was a Zelda game. And if they reskinned it back into Zelda for the west, people would say it's not technically a Zelda game, and you "can tell right away because of how different it is."

Bottom line is, Mario 2 was more than just a concept. It was in development to be the next Mario game and had a gameplay engine with several gameplay systems already created after it left the concept stage. The Captain Toad concept however never left the concept stage for a Zelda game because they didn't find it suitable for Zelda. How much of Mario 2's gameplay was inspired by Doki Doki is unclear. But Mario 2 is at least partially an actual Mario game, from a technical standpoint. It's even possible that all of it is, and that we could just as well say that Mario 2 was reskinned into Doki Doki, and then reskinned back into Mario 2. Things similar to that also happen some times, like how Contra was reskinned to robots and renamed Probotector in Europe.
I'd love to read an interview with the developers of Mario 2/Doki Doki though to see how much of it is Mario, and how much is Doki Doki from a technical standpoint.

Again so? It was released a non Mario title so it's technically not a Mario title it's Doki Doki Panic and was reskined in the west that's a fact that can't be argued, an early prototype doesn't change this as many games start off as something else and Captain Toad is an example, final release is all that matters in this case.