iOS 10.3 with APFS has been in public and developer beta for several months - it's up to beta 7 right now in fact. If this were as vast a problem as Micheal Tsai presents in this post, wouldn't we (the devs and beta testers) be running in to this a lot?
Given how loudly the tech press proclaims any perceived mis-step by Apple, I'd have to believe we'd have been reading tons of 'Apple is Doooooooomed' articles about this by now. Given that this hasn't happened, and I haven't seen similar problem reports on dev forums and other hangouts, I'd lean towards there being some miscommunication or misunderstanding here.
This is not likely to be a particularly big issue on iOS, because the file system isn't directly exposed to the user (and therefore the user can't go making changes behind the app's back). There are of course still edge cases that could cause a problem, but they're going to be relatively rare.
But this may become a much bigger issue when we start using APFS on macOS.
As I understand it, it may only be a problem when using the straight libc calls. But most devs just use the file system stuff that's in Apple's Foundation framework.
Given how loudly the tech press proclaims any perceived mis-step by Apple, I'd have to believe we'd have been reading tons of 'Apple is Doooooooomed' articles about this by now. Given that this hasn't happened, and I haven't seen similar problem reports on dev forums and other hangouts, I'd lean towards there being some miscommunication or misunderstanding here.