RIght, so using Spotlight is not the same thing as using the Finder. Spotlight ends up using the "native" application to open the files.
Yes, the Finder opens files in their "native" applications, but only at the most basic level. For example, browsing for a JPEG file in the Finder, if you double-click the file it will open in Preview. If you double-click the same file in Spotlight, it opens in iPhoto.
Actually, it would be nice if Spotlight provided more...