Yeah but NeoGAF experts have spoken: Nintendo doesn't care about it and neither should you.
I mean, personally, I think it takes away from the story of the games and sort of pushes towards smoothing the rough edges when the incongruities are part of the charm. The idea that there is one perfect timeline that makes sense tends towards retconning and repurposing of previous games and game elements, when a looser, more 'legend' like approach to the fiction that is also more in line with how the games are made, saves you that pain and trouble. And it is not like there is a gripping story there, which is only found in everything fitting together but not in there being a loose connection between things.
IDK. There are plenty of people who call you out for this attitude too, including on GAF. Gotten into long discussions where people took umbrage with me not caring much what the official timeline said.
I guess my main point is, sure buy into the timeline if you want, but there is plenty of reason not to care about it if you don't like it and you really won't miss anything from the games if the price of admission to the timeline looks too high for you and you don't pay up.