Hello,
If you haven't seen it already, here's our guide about packaging & installers: https://itch.io/docs/itch/integrating/compatibility-policy.html
Generally, we believe that if you think your users are going to have issues installing your game from a zip file then we recommend you point them to install through the app. There are a lot of benefits, it does a lot more than just extract a zip file for you. Writing your own installer comes with a lot of pitfalls (described in the guide above0.
We do understand though that this isn't ideal, since some people aren't going to read and will end up grabbing a zip file and not know what to do with it. In the future we'd like to explore having our patching backend that handles patches build self-extracting installers.
We don't have a way to mark files for app only/for web only right now. One option might be having a way for developers to make downloaders confirm they want to download a zip instead of making the download button so easy to click.