a) Tooling: yes, it's still much easier to debug a native app than a pseudo-native app.
b) "Emulating native leads to bad UX": this section is absolutely right. Stop hijacking scrolling and building in cruft.
c) "Hassle-free web": absolutely right. You don't need an app for that. Just give us the information and let us have the basic interaction we want. No, you shouldn't present your menu as a PDF either.
d) News: this is where I disagree. Users don't go to news sites so much; they go to aggregators which link them to individual articles (reddit, facebook). It's hard to deep-link into an app. This is a case of the app existing to further the commercial needs of the content provider (increase lockin, ads and tracking) in direct opposition to the wants of the user.
People keep trying to make the "magazine app" happen, and I've seen very little evidence of it working.