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.
App processes are sorted in order of most recent use, keeping the most relevant ones at hand, and those that aren’t used for a while just silently go away without much fuss.
In comparison browser tabs aren’t organized unless the user does that themselves, and so with each web app tab management overhead increases. Some browsers have an idle tab auto-close feature, but that closes the wrong tab (usually a page with info pertinent to something I’m working on) quite often. “Installing” PWAs can be an ok-ish workaround, but the problem there is that a lot of sites don’t have the little bit of manifest magic that makes saving to home screen “install” a PWA instead of just opening a browser tab.