I agree that it seems that RR only wants to go down one level to look for the art.
You may want to visit this thread. I asked Guino the question about the directory structure and he didn't reply; I know he's got a lot going on.
Centrafuse handles album art browsing beautifully. I'm using the same directory structure as you and when I go to album view it lets me scroll through my 1500 album covers. Centrafuse makes you name every cover "Folder.jpg", so I'm sure David has just written some code looking for that file anywhere in the path. IF RR had the same clean browsing and searching features that Centrafuse does, RR would be a no-brainer. Unfortunately, I don't have any coding ability so can't implement these features myself.