Huh, on my Arch PC there's no even a request to accept the invite link within the browser, as long as I have any (mine, official) Discord client opened (i.e. browser does just redirect me to the opened client in order to proceed), with the closed client though there's a request to log in and with that I can accept the invite link within the browser. So again, no XDG or custom protocols are involved for me. So really I have no clue how you're doing this.

I should be saying that I use Firefox and X11 for testing, but I'm more than sure that whenever I would use Wayland or X11 it won't matter, webpage shouldn't have a way to detect this and behave differently. So I have no clue how to even trigger Discord to use their protocol over WS without setting up anything extra. I've been also using the discord package as of the client.

Also from what I see with the steam, you can register the protocol with MIME and .desktop but discord does configure neither of these. So it doesn't seem like this would be a thing anymore, but again I might be mistaken or maybe Arch packagers don't want from Discord to register their protocol, I dunno.