100% API access has nothing to do with template apps. It’s just not what they mean. Template apps are generated apps which consequently look very similar (depending on the service that’s being used). For instance, a service that spits out native apps based on a WordPress site would generate very similarly looking apps, where probably only the content would be unique.
The 100% API access feature has been discussed before and wasn’t considered a problem. Also, Apple has (to my knowledge) never rejected a NativeScript app because of it.
Note that with regular Java/kotlin/ObjC/Swift and even RN/Cordova you can get access to all API’s as well by using reflection, and you can even obfuscate that code if you like, to hide it from Apple’s review team. So I think all those frameworks share the same characteristics in that respect.