I've also seen conflicting information that GOTY either has all the patches, including the final, or it doesn't. I've also seen it said that you're not 100% patched unless you install the SI disc. I can't speak to that since my copy of Oblivion is original retail, from before they were forced to update the ESRB rating.
Usually when I reinstall I put the game in, then the contents of my KOTN CD, then the SI CD. Once all that's done, I install the final official SI patch. Patches being cumulative, they contain all the changes from previous versions and you shouldn't really need to sweat any trivial differences in the BSA packs or anything. You will not notice whatever the differences are when you're playing.