Re-read my posts more carefully Baratan, because it looks to me you do not understand what i mentioned in my previous posts. (At least that is what i am thinking right now.)
You're going to have to clarify what you're saying.
Creating a clean save is something that must be done by the player manually. It's not something the game or Steam can do by themselves. The player must load their game without the mod, save their game, and then load their game with the new version of the mod. This hasn't changed since Morrowind and hasn't changed in Skyrim either.
Now, it doesn't matter if the player is informed that they need to create a clean save at launch or when they load their game. In fact, such information at launch may be inaccurate if the player is using a different save than they did previously with that mod or are creating another character. However, if the message box appears when the game is loaded and the player gets in-game it will be accurate in telling the player that he needs to create a clean save before using that mod. It takes a couple minutes for a mod author to create a message box that pops up when the player loads their game.
Simply put, if a mod author creates a version of their mod that requires a clean save that author should have a message or message box appear when you get in-game telling you to create a clean save. Oblivion mods that required clean saves often did this. It's the mod author's responsibility to inform their players that they need to create a clean save before they can continue. There's no way that Steam can do this on it's own.