Never heard of anyone getting a bad file from an Apple download. Many report problems when using SU. I have sometimes used SU to just do the download and do the update later. Never had a problem either way, but you can't be too safe! For example, I never update/upgrade anything without first making an archive of the original first. OS X makes it so simply easy right in a Finder Window. That way, when the update/upgrade doesn't work or causes problems, I just delete the new file(s) and un-zip the old one. And you don't need Time Machine to do any of that.
Of course, all the files Apple sends probably come from the same server whether one uses SU or a direct download, so the whole exersize may be moot!
However, the biggest problem with SU, IMHO, is that it leads people to make installations before thinking things through:
Do I have a recent, working backup of those files?
What, exactly, will this update do and to which app(s)?
Am I doing anything besides making this update? Back ground activities may conflict with the update or a required Restart may not save the work done in that back ground process.
Can I afford to fix a problem right now or would it be better to complete the project at hand?
Many of Apple's updates require a Restart, if you agree/select several of those at once, you may not know which one causes any problem that appears at the end. Best to do those one at a time, IMHO.
