somewhere i saw that someone was considering developing an extension that would download, unzip, and install updates to extensions; but they were taken aback by all the possible 'bugs' caused by nonconforming addon-uploaders, and addons that require special instructions. (I think maybe it was minisweeper.)
well, i think that what you could do is host a database of all the known addons that WILL work with the update extension, and the version #s that have been tested to work. You could also include ones that work except for special instructions, and allow the end user to bypass if an extension isn't in the list. (attempt an update, even if it might not work). Another idea would be to bounce back the results of each auto-update to said database, so it becomes virtually self-managing.
another idea that JUST popped into my head would be to allow extension developers to write scripts that execute on an update, so as to eliminate the 'special instructions clause'