It's definitely one of the more salient counterpoints, but I think it's more the kind of thing that will limit the market size, rather than kill it altogether. The observation that Rolex sells $20,000 watches with the same internals as a $6,000 watch is where you'll find the counterpoint to the problem of obsolescence.
Yes, the Apple Edition watch will likely suffer from the same obsolescence issues as iPhones, but as others have pointed out, that will only matter for certain types of buyers. The market for $20,000 watches is pretty small, and it's composed of different types of buyers. The smallest of the market is the group who can fork over $20,000 annually for a fashion accessory, rather than buying something as a milestone that will become an heirloom.
However, Apple can absolutely afford to build a very small number of Edition watches when selling at this price point, because the cost of materials is so low, and they'll sell tons of them at lower price points, which gives them the scale they need to justify production. This is where the correlation to the ubiquity of Rolex movements come in. Apple is using the same strategy. They have one "movement" (a computer in this case), which they're packaging to suit a very broad set of price points.
I think Apple will succeed in this endeavor because they have the brand. Rolex is, again, a very good comparison. In really uppity horology[1] circles Rolex watches are considered pedestrian because they are mass-produced, and they don't include a lot of hand finishing like the more prestigious brands. That doesn't appear to matter to the broad market though, because Rolex enjoys two logic-defying distinctions: 1) they sell many more watches than any of their upper-crusty close-kin, and 2) their watches hold their value in a way that defies their mass-production status. Sound familiar?
Apple products are often lampooned for selling at a price-premium when compared to similarly specified commodity alternatives, and Apple devices fetch strong pricing on the secondary market. IMO, Apple & Rolex are as close as we've seen to companies who have deconstructed and are in the process of perfecting the formula required to bring to market products that uphold these attributes. If Apple can do this successfully with watches, they will have upped the ante significantly by jumping from one vertical to another; a feat for which I cannot think of another example.
1: Technically, the science of timekeeping, but often used to refer to the community of people interested in timekeeping devices (watches).