Web apps can ask for your location or microphone the same way native apps can. Just reject it, there’s nothing that says you have to accept on either platform, so to say that’s a negative for native apps is odd.
The biggest downside of native apps is you can’t customize them with extensions or user styles like you can with websites.
Tabs are a big win for mobile web, I agree. I just don't think it outweighs the annoyance of navigating the app in more traditional ways.