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.
I've found it to be the opposite. Perhaps if you're heavily involved on Reddit, LinkedIn, etc., then it's more convenient. But I only go to those sites via a search link. Why would I want to spend time and effort installing the app, just to see the same content I just landed on?
It's a huge red flag when websites push their app so intrusively. It means the app has little value and will be just as bad or worse when you use it.