MediaWiki:Fileexists (a message about overwriting an existing file, when the user has permission to do so) should be shown on Special:Upload whenever it applies. Currently the message is suppressed if wpForReUpload=1 is set (as it is from the "Upload a new version of this file" link below the File History). Just because the user has specifically said "I want to reupload" doesn't mean they shouldn't be reminded of the rules for doing so.
Alternatively, since the main motivation for this bug is Commons' need to remind users of its overwriting rules, there could maybe be a different setting, wpForSharedReUpload, which is used on shared repositories like Commons, where stability of images is more important and so not overwriting images when you shouldn't is more important. And that setting would either display MediaWiki:Fileexists or a new message.