Part of the confusion with the documentation about this is because I used to keep a copy of the skins in svn and in release packages at /Data/Sites/1/skins in addition to the copy at /Data/skins.
Over time this became too large and cumbersome maintaining the files in both places though it did make the release packages a little less problem prone since this copying of files at setup occasionally hangs up or times out on cheap hosting.
So now I would say just develop your skin in place at /Data/Sites/[SiteID]/skins/[skinname]
If you can put that folder under your own source control great, if not then periodically copy it to a folder wwhere you can keep it in source control.
So yes, its not currently a risk that existing skins will be overwritten by upgrading, though at one time I did warn about that because we were including skins ay /Data/Sites/1/skins in the packages.