I looked into this a bit more, and at least this time I have a well-defined question.
I'm trying to fill the RGB channels of my image with data, while keeping the transparency at 100%. Using the "More" button on the Colors window, I can set the transparency of my colors, but when I set the Alpha to 0 it doesn't seem to be filling in the RGB channels with any data. This is difficult to tell directly from Paint.net (after all, how can you tell if something is there if it is 100% transparent), but it is obvious when I load the file up into Unity (or another app that is sensitive to what is in the RGB channel even when the pixels are fully transparent.) Setting a transparency value of 1 will fill the RGB channels with data in Paint.net, but setting the transparency at 0 will not fill the RGB channels.
Does this make more sense? Is there a way to fill the RGB values with data and have 100% transparency?