I had some similar concerns about Tobi potentially being related to the Whirlpool village. Perhaps the true Madara's half-breed son by a Whilrpool woman. It's all very circumstantial but looking on the old ninja world Map the Whirlpool Country is right between the Fire Country and the Water country. We know that country was destroyed in one of the Ninja wars and the survivors scattered, and we know that Tobi has been recognized as a former Mizukage. It's plausible that he could have escaped the Whirlpool country and hidden out in Water, rising through the ranks of their Ninja until he was in charge of everything. This theory doesn't explain why he'd bother rising through the ranks of the Mist but it could explain why he's so butthurtt towards Konoha without him being quite as old as he claims he is.