
The Tile Set Editor Preferences have the following option for Auto Tiling:
The section for Confirm Dialogs has one preference:
This controls the default behaviour when changing the Tile Width or Height in a Tile Set. By default this is set to "Show Message", so if you try to increase the Width or Height in a Tile Set that is being used in a room, it will alert you with a dialog message that such Tile Maps will get cropped (as the room can now hold less tiles). You can set the default behaviour to "OK" which will skip the dialog and always allow such modifications to the Tile Set.