Nobody is saying there are not incentives for Japan to try and grab Spanish America. But just because somebody wants to do something, that doesn't mean they can do something.
And if Japan tried to develop California as a colony as a forward base to attack Mexico, there are several issues. For starters, Tokyo to San Francisco isn't appreciably shorter than Tokyo to Acapulco, so logistics are still going to be an utter pain, with serious wastage in men and material.
This is going to take a seriously long time, decades at a minimum, which gives the Spanish plenty of time to discover the effort and prepare. And Madrid (and definitely Mexico City) will be able to hit California faster than Japan can reinforce.
This is also ignoring the fact that San Francisco bay wasn't even discovered until 1769, long after Japan went isolationist.
Seriously, why are people thinking that Japan could sustain an army numbering in the tens of thousands over an eight thousand mile long supply line that takes six months on average to traverse? Because they either have to do that, or enact a plan that will take at least half a century to come to fruition, and no government is that patient, and which could be wrecked by Spain in the exceedingly large window of warning.