Hmm...I haven't used Everything integration at all on DO now, so I don't know what it does there.
I'll admit, I haven't fully thought this through. Right now, I just have the Everything client running, I just don't have it configured to scan my local disks at all. I literally use it as a client to the instance running on my NAS. I take advantage of the "ETP Client path rewriting" feature. This way, the results that are returned don't come back as relative local to the server, but UNC paths. i.e. D:\foobar on the server is returned to my Everything client as \server\foobar and since that's a valid path on my client, clicking it works, which opens with the default file explorer tool(for folders at least), so DO. So there's a shallow integration that way just via Windows defaults.
From a search perspective- I don't run Everything local for searching. All my important stuff is on my NAS, which is why I do it the way I do, so I'm not a good one to ask there. I only ever worry about searching the NAS, so I don't have a good response on what the most useful behavior would be with regards to running a global search that might encompass both local and remote results. I've only been considering it from the search results coming back from the server.
I think search remote/autodection would be great, although it might be messy. I didn't realize before that they apparently do it all over FTP some way or another. It does look like they've just given in and tried to utilize the default FTP port, and that is where my instance is listening. The tricky part here may be whether you use the FTP based interface(probably better) or the HTTP one, which would likely require a scrape? I think it's reasonable to say we would have to do some configuration though...Everything itself isn't quite just click some buttons to enable that stuff, so having to do some config on the DO side doesn't seem out of place to me.
I would think that having it happen automatically, i.e. use Everything if Everything has been configured, but you may be right where a list of instances might be needed? I don't have a complex enough situation here(i.e. multiple file servers) where that's really a concern. That's probably more of a you question for what your user base is like as to the best way to handle that.
Maybe just a checkbox to try and use Everything if available?
The Everything searches come back so fast, I guess it doesn't seem to me to be a big deal if the remote instances are included in a global search. Maybe the question to ask there is, why wouldn't you want to include them in a global search? The normal response to me, is it would make things much slower, but that would defeat the purpose of Everything, wouldn't it?