because theoretically is still tobi

That Madara has no village that's why he has "?"

At that time of series no one actually knows who he was. He only claimed to be Madara Uchiha.

Whilst I am aware of that and that does make sense, why would masked man be considered a Konoha ninja even though his identity at the time was also unknown?

You are actually right. Technically, Minato was the only one who saw and talked with the masked man and he came to the conclusion that he was Madara. If that is the standard used as a basis for masked man being listed as a konoha ninja then madara 5kage should fall under the same category as well. This is an interesting topic

Tobi is not a konoha.

Madara 5ks is tobi so that's why is not a konoha.

Masked man is not tobi, it's the version in the past that unleashed kurama.

That said all of them are obito so you can't use two of them together.

Otherwise why hokage minato is not a jinchuriki?

He was still hokage when he died after having taken for himself half of kurama.

And why tsunade sannin war is not a senjutsu?

Why sakura gnw is not senjutsu?

Both of them were perfectly able to enter in their sage mode at that time.

There are a lot that don't match.

Minato was not able to use even use kurama's chakra because he died right after so it's understandable if he isn't a jinchuriki. Both sakura and tsunade don't have sage mode. The hundred healings jutsu does not use sage chakra but rather chakra they have stored up in a long time.

And I don't think the basis for madara 5kage and masked man not being listed as konoha is the tobi identity. It might just be a discrepancy on the game makers' or developer's part.

Whilst everything you say makes sense and is true, my question still remains as to why masked man would be a konoha ninja, and madara five kage not, even though both are 'unknown'. Shouldn't masked man have the confusion attribute as well rather than konoha. It seems the best option here would to be to just accept this if nothing can be changed.