While it's easy to dismiss some of these as niche, many of them such as file system access and USB device support would completely change how some software could be delivered.

By not supporting these, one is forced to make a native app in many cases. With support for some of these standards, entire classes of application could be delivered via cross platform web applications. Imagine being able to install firmware updates on USB devices just by visiting the manufacturers website, for one.

While we can argue about safety, the file system access problem can be solved in the exact same way apple solved it for native apps, with permission dialogs etc and only exposing the selected items when attempting to access resources on the device. This is indeed the approach Chrome/Edge use today.

If you look at the browser API specs Apple has chosen not to implement and Chrome/Edge has historically, it's hard not to feel Apple is trying to protect its own native app store at times. There are obvious self-interested reasons for Apple to protect it's own store/native app system; even "free" applications often generate revenue from in-app purchase transaction fees or subscriptions. If developers can more easily avoid shipping a native app, they can also more easily avoid paying Apple fees.