They can flag antivirus signatures just like everything else, and I've experienced this happening in the past. In the end, extensions are just some javascript/css files in a folder and they get scanned just like everything else.
> Extensions autoupdate
So can any piece of software if it wants to. It's trivial to make an updater start on boot.
> It is not uncommon for large spyware companies to buy up a bunch of the most popular chrome extensions, and proceed to inject them with malware
The same can, and has, happened for "regular" software.
> Since an extension runs inside your browser, it's much easier to forget that they're essentially always running, whereas once I exit a desktop app it's presumably gone
Desktop apps can trivially just not show a window if they want to. They can trivially add themselves to autostart. It depends entirely on what they're doing, just like an extension.