To be totally fair, there's actually a good reason for that. Having a warning pop up every time you load the save is a quick and easy way to identify if a save has been edited. That way, whenever John Idiot™ totally breaks his game by fucking with flags and goes crying to the forums about how the game is bugged, the devs can ask for a save, get it, take one look at it and go "oh, this save is edited and this guy broke his own game, it's not our problem." I may not be a coder, but I've been involved in game development for long enough now to know that being able to weed out user error in bug reports is honestly a very valuable tool.
That said, they could totally have it be less intrusive and just have a variable set somewhere they can quickly look for to know if the save is edited.