Supermarkets aren't nearly as monopolistic as app stores. A supermarket "user" is free not just in theory but also in practice to use competing stores (and many people really do). Not just that: in most places, there
are competing stores, quite a few of them, not to mention alternatives like online deliveries. If a goods producer can mass produce products for a supermarket, they're likely also capable of paying for super-market independent marketing; i.e. they have independant channels of communication with the consumer, and can use tools like MSRP to suggest reasonable prices to avoid price-gouging by the supermarkets, and the difference in customer access to ads by the store or by the manufacturer isn't huge. Additionally, a supermarket provides a valuable service to the producer beyond merely locked-in network effects: transporting tons of goods that last mile and distributing them to individuals requires quite a bit of work.
Compare that to app stores: users are in practice not free to pick another app store, even on android - network effects make using alternatives quite tricky and even risky, and the device/OS maker don't make it easy to pick reputable alternative stores. App stores additionally leverage their monopoly on that user to hide their costs from them; e.g. in apples it's not even allowed to mention the cut apple takes and where you might be able to buy more cheaply - and not just in the store, but even in the app itself, even indirectly! There's no MSRP by which to note that that 30% cut is extortionate. Finally whereas last-mile logistics are tricky for real-world goods, app store checkouts are not; almost the entire value provided is in network effects: i.e. the value is provided by the users of the app store, not the app store itself.
All of these disparate factors mean that app stores clearly are not a competitive market, whereas supermarkets aren't quite as bad. But let's not forget: just because supermarkets are "less bad" than app stores doesn't mean there's no potential for market manipulation; we should be vigilant there too - just that the kind of manipulations supermarkets can pull off aren't going to be quite as impactful.
TL;DR: not only are app stores much, much worse than supermarkets when it comes to harmful market manipulation, flaws in one market do not excuse flaws in another anyhow.