Hey there. Having been through this particular mess myself with one of our apps, I can tell you how we were able to solve it, and what eventually stalled the release of our app on iOS. Like you, we did the webview wrap. We used GoNative, and it was an expensive, but good solution. We got through Google with no problem, and then got exactly the same message from Apple. We added push notifications, and got the same thing back. What finally got us through this part was just making a change to the very first page that displays on mobile, and taking away the browser bar.
So, we compiled a second build on GoNative (they don’t charge to do more builds of the same app) and set the landing page to an iOS specific login page that was created in bubble as a mobile page with the “native app” checkbox checked. We then set the app to remove the browser bar. I don’t know what solution you used to wrap your app, but GoNative had an option to remove the browser bar from the webview. They also have option for “native iOS functions”. We switched on the one for Native navigation menu, and set the URLS for each button of the menu to the specific pages of our app that they’re supposed to point to.
All of this so that when the user logs into the app it LOOKS just like any native app. No browser bar, and nice iOS style navigation menu for everything. We didn’t even need the push notifications. It’s that the user experience has to look like it’s a native app, and not a website.
What actually kept us from releasing in the app store, as of now, is payments. We have a subscription service, so Apple requires us to have Apple Pay integrated to accept payments. Even if users can only sign up for the service at our site, and don’t accept payments of any kind in the app itself, Apple requires us to have that option available to users. And, of course, so they can take their cut of every subscription. At this moment in time it wasn’t something we were willing to do from a business standpoint, or a technical one. So, for now, we’re happy on the web and in Google Play.
So, just to your main question, if you can remove the browser bar in your build, and add native navigation, that was all it took for Apple to approve us past the “need more native functionality” point.
Here’s a few screens of the app with the bars removed, so it looks like any native app.