Jeff is correct. It should be server wide and individual resellers should be able to change this as well. Note Server wide changes would not affect changes resellers have already made.
If you have your own skin you'll have to keep it up to date with the latest DA release. This is a bit of a pain.
Being able to simply change the header logo at admin level (So it is seen in the resellers level) and at reseller level (so the resellers users can see it) would seem to be a better and easier to maintain option.
I'd like to see this happen as a first step to a more easily re-brandable DA as having to take the time to learn about skins etc etc is not feasible for me. However I would see it as a great option to offer my resellers if it could be done simply. Currently it's out of the question unless they want to learn how to skin too.