Would you choose to pay Hey's subscription $142/year to be able to pay on the App Store, instead of $100/year paying on the web? Or if it was available, would you pay Adobe's Creative Cloud for $906/year in the App Store or $636 on the web?
I'd choose to pay slightly more for the convenience for very small subscriptions too. But for large ones that's too much difference.
If a service was literally doing as you say, charging more through Apple's App Store vs their site, I would choose not to use that app. At all.
Part of the real appeal is the pro-consumer parts of the App Store. Like I said, being informed before renewal is something that very few services do but Apple does for any subscription.
Edit: to be clear, I think even $99 is too expensive for Hey.com. This is my opinion. Some people may find value there, but I don't think Hey does enough to justify being more expensive than Fastmail (which also has important features, to me, that Hey doesn't).