The Tile Set Editor Preferences has the following option for Auto Tiling:
Auto tile background colour: This option sets the background colour within the tile set editor in the section for creating Auto Tiles. The default colour is (rgba) #808080FF.
The Tile Set Editor preferences also has a Confirm Dialogs sub-section:
The option available here controls the message that pops up when you change the cell
size of the tile set and this will affect how the room tilemap layers are rendered (resulting in cropped layers). By default you will be prompted to continue or cancel the operation, and this option lets you suppress this message by selecting "Okay"
which will go ahead with the tile set cell change regardless of the impact on room tilemap layers. Default value is "Show Message".