I was referring to the WeChat web app vs. the WeChat Mac/Windows app; the web version has no access to your filesystem, but they are not allowing people to use it anymore. The Mac/Windows versions could theoretically read any files on your system, spy on your clipboard, portscan your private LAN, scan Wi-Fi networks, and lots of other nasty things that the web version cannot.
Also with webapps it's much easier to inject JavaScript to "edit" their behavior. Desktop apps are often compiled to machine code (or have mysterious pieces thereof which are) which makes it difficult.
True, but in terms of privacy, that doesn't matter if the app can't communicate out.
I agree with you for purely offline tools such as Inkscape/GIMP/etc. though.
True. Apps that must communicate out in order to do their jobs are a different category.
I strongly prefer native apps over web apps because I can firewall off native apps. I can't do the same for web apps.