Sometimes a user can make edits that go unnoticed for a while, and Special:Nuke won't be able to find them because they aren't in the recent changes table anymore. I think it makes sense to have Nuke be able to deal with these cases;
I understand that maybe doing that would require rewriting significant parts of the extension. If someone can confirm this, please change the summary of this bug to a request for a new extension (similar to the request at T15601: New extension to one-click revert all of a user's actions in recentchanges).