Regardless of how you perceive making it, the representation is still (nearly always) a color underneath an alpha channel.

If you inspect the image in a full-featured editor like Photoshop or GIMP, you can inspect the channels individually or remove the transparency entirely to see this fact.

I think with most GUI programs, the eraser and cut tool will leave color as what it was before it became transparent.

EDIT: saurik has a good point that I forgot about -- many editors may actually throw the colors away when you export unless you ask them not to.