You have only 1 transparent color, but the problem is in trying to locate
which color. If you have an image that's red, white, and blue and you want the blue sections transparent it's easy. What if your pics has several shades of blue? In order to figure out which one is the one you want to be transparent, you may well have to try a dozen times.
Take this pic for example:
http://allspark.net/cypherswipe/trans-test.png There are dozens of near-black entries, trying to find the palette entry which will change the black background to transparent is hit & miss. You might get the right one, or you might just make one of the shadows in the middle of the image transparent. With the other method, you could simply click on the background and it would automatically choose the right palette entry.