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.
On the other hand, for mobile apps, there is still a device-specific mentality.
Imagine web apps being built with a different flavor for all the major browsers...
I hope that the same level of standardization comes to mobile apps too with the option to use more device-specific features on top of the generic UI.