Yes, that's the "workaround" I use but by default people are expecting to find something in the app store.

> They probably dont know the difference between an app rendered with a browser or a truly native app.

Absolutely, users do not know or care what technology you are using so long as it meets their expectations of use. Users are going to the app store as a discovery mechanism for "something that gives them an icon on the phone to get to that thing", most have no clue what "native code" means.