I think the current way to export and save scenery is ok, it doesn't require a lot of work and is not too hard to understand. I have a tutorial for it here:
http://forum.outerra.com/index.php?topic=3231.msg36246#msg36246However, it's true, some control for the end user would be nice. Currently, all the scenery data is stored in the main cache folder, but I guess in the future this kind of content will be separated from the user cache data, like it will probably be the case with other datasets as OSM.
Something like : username/Outerra/sceneries/moddername/logic path to the modified tiles (+x/47/6F/E7/00, etc.). That way, it will be easy to delete a scenery, because it will be in a single place, not mixed with user data or with other scenery content.
When it happens, maybe adding an objdef file into scenery package could be interesting, with a custom interface (like the vehicles/models one) so the user can check ingame which locations are installed (maybe with the possibility to remove these, so he don't have to explore the files), with a list of the dedicated campos.