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As far as I remember protocolhandler is only used for the client detection. I don't know for sure but I don't think that would have any effect on the domain pass through. What are you seeing or trying to achieve?

I am trying to get rid of the "Detect Receiver/Workspace" button and in past i have just disabled protocolhandler in the web.config but when i did it domain pass through on MS Edge/Chrome seemed to of broke and i found this https://support.citrix.com/article/CTX269089/domain-passthrough-does-not-work-with-microsoft-edge-and-google-chrome

Oo not seen that before, real shame it doesn't go into very much detail. Maybe in that case I stand corrected. But I still not seeing how client detection would break passthrough unless protocolhandler does more than client detection. I'll see if I can give it a whirl in my lab.

At my last place, we tried every fix that I could find to get domain passthrough/SSO working in Edge/Chrome, and nothing seemed to work.

Yes I know that the OG edge could not do passthrough at all, but I thought they fixed that a couple of years ago. Maybe protocol handler has also something to do with the ssonserver workspace component but that would only stop the vda sign in from working not the storefront iis bit as far as I remember.