New in-content install confirmation will (usually) show before the download starts, so we can potentially save the user some time that confirmation just tells them if that addon is already installed. Related: bug 726965.

How can we do that if we don't have the XPI to be able to see what its ID is etc.?

By getting AMO to pass in more metadata about the install. That's needed anyway, to be able to show a confirmation before it's downloaded (as a push to avoid making the user wait for the download to complete). Installs without that extra metadata will get the download progress shown first.

Can this warning be conditional (even on a hidden pref)? I install the next nightly of lightning.xpi and gdata-provider.xpi every day; it's a different build every day, but the Extension IDs are the same and the extension versions change only rarely. I'd rather not have to click an additional confirmation to what already exists.

Per policy at https://wiki.mozilla.org/Bug_Triage/Projects/Bug_Handling/Bug_Husbandry#Inactive_Bugs. If this bug is not an enhancement request or a bug not present in a supported release of Firefox, then it may be reopened.