Of everything that irks me about the app store (and I say this as someone who uses almost exclusively Apple computers / mobile devices), this is pretty high up there. It makes it damn near impossible to run a successful marketplace businesses on iOS: if your business is based on skimming a percentage fee off the top of your user's transactions, Apple taking 30% is more often than not a dealbreaker.

That being said, that's not an issue of native apps vs. web apps. If you want your application distributed through the app store, anything payment-related (or even potentially payment-related) needs to go through Apple's payment services. Period. Apple would complain just as much if you had a native app that had your own payment form, and they'd be 100% fine if you built a pure webapp (i.e. not on the app store) that accepted non-Apple payment.

> because a webview inside the app had a payment form

You didn't get rejected because it was inside a webview. You got rejected because you were selling something outside of In-App Purchases. You know this.

Why do webviews have anything to do with it?

That's insane, I just had the same 2) rejection and spent literally weeks thinking that I wasn't able to properly explain what the codes where for, because it didn't make any sense for them to reject that. But since you've had the same issue, i guess they really start to be seriously deranged.

Whilst that's arguably true, UIWebView being the poor cousin of mobile Safari isn't evidence for it.