Repeat Signage presentations
The transparency colour is used in Repeat Signage presentations to make your control partly invisible so that you can have a custom irregular shaped control. This only makes the exact colour transparent. For example, white and an off-white like ivory are different colours. This is different to fade which is used to make the entire control transparent to give a ghost effect.
Repeat Pictures
If you are creating Repeat Pictures, then if you are using a picture that has a transparent background, then my default the background will be white in the designer. If you select the 'Default transparency colour' option, then this tells the designer to make the background transparent instead.