I've taken care of these except I am leaving the Gallery... one in there. The setting will show up if it is added to the GalleryModule settings. Its a "feature" to support hosting situations where its not possible for web code to create folders beneath Data/Sites/[SiteID]/GalleryImages
I don't include this setting by default because I think it is best when possible to use sub folders for gallery module instances, but if I get a support question about it I can tell a user how to add that setting. I've only ever had 1 user who needed this but I put it in there for him but didn't really want it in the UI under normal situations.
Thanks,
Joe