I think this isn't as true as it used to be. Sure, SF and whatever the two others you were thinking of are massive, but there are smaller scenes in other places that also have funds available for incubation-type environments.
At the very least, understanding what the process is supposed to look like will help folks in those nascent scenes identify when something is amiss.
Half the value is in funding, the other half the network. You have an exponential decrease in opportunities elsewhere versus San Fran (and Seattle and NYC). Forcing, or at least strongly encouraging founders to seek out incubators as the One True Way will restrict, not increase opportunities for founders. What YC is doing is dressing up VC ideology as something that is universally founder-friendly. What's good for the capital owner isn't good for the founder when the founders do not have many options to choose from in the first place. In those situations it is better for the founder to keep more of their pie to themselves versus selling out to the only player in their very local, very small pond.
At the very least, understanding what the process is supposed to look like will help folks in those nascent scenes identify when something is amiss.