I would like to second the "complaints" about the tray in its current state.
I really like HoudahSpot and try to use it more and more and I am especially very happy about the included tagging facility, but after a couple of weeks of using the new version I have to say the tray is more of a hindrance than a benefit.
I have the tray flying out quite a lot, but it is mostly accidentally and only very rarely by intention and this is usually quite annoying because I have to move the mouse out of the way and wait for it to close again, before I can continue with what I intended to do. Especially with using Mail it is a massive hindrance.
If you really want to stick with the tray, could you possible change its behaviour? Do you know Barebones Yojimbo? This for example also has a tray for ingestion of items into Yojimbo, but this tray only opens if you drag something towards the edge of the screen, but never when you only approach the screen edge with the mouse pointer. Additionally it has a transparent flap protruding slightly into the screen, which opens the tray permanently on clicking. This is so far the best solution for a tray that I have seen and the only further improvement that I could think of right now would be the ability to configure the size and the position of this flap on the screen edge.
I have attached two screen shots of Yojimbo's tray (closed and open).
Additionally I would really love a solution like the one described by Jono, I mean a shortcut invokable tagging window at the current pointer position, maybe HUD style. I think the tagging should be available from within HoudahSpot's results window as well, maybe just a button to open a tagging window. It would be (closes to) perfect if this tagging window would be available via a system wide shortcut (as a service).