Actually, that isn't the biggest problem. Yeah sure, an in-app privacy policy is a problem for a developer, but I'm sure that if you've submitted your app to the appstore within the 30 day limit and it's denied by Apple because of a different reason, a judge will probably take that into account when deciding on that issue.
No, a much bigger issue in the difference between in-app or an in-store privacy policy is for the consumer. If the privacy policy is in the store, you can read it and assess it before downloading and installing the app. If you don't like the privacy policy, then don't download and install the app. If it's an in-app document or link, then you have to download, install, run, possibly even create an account an login all before you get to see the privacy policy. By that time, the app has probably already completely sucked all personal information out of your phone and submitted it to the app owner.
Same with a EULA that's presented to you when you install a piece of software on your PC. That EULA is presented to you after you've bought the software. So if you don't agree with the EULA, then I'm pretty sure the seller is forced to completely refund the software to you. It's basically the same thing as buying a bread from the baker and after paying, the baker says that you are only allowed to eat the bread at home, and only if don't put any meat on it.