It depends on what you are using the design for. If you are using it for a shirt it does not matter what you do to the background.
A designer could make the design background clear (or transparent) but printing the design will work differently.
Picture it like this - if you are printing the design to a light transfer, than any white (or lack of color) will be clear on the transfer. (or in effect the shirt color you are putting the design on) Even if the background is transparent on the computer, since it has no ink (or color) it will be clear.
Now for a dark transfer, anything that is white (or lack of color) will be white. So even if the designer puts a transparent background on the design on your computer, it will still be white on the iron on. A dark transfer is like a regular sheet of 'white paper' - if you printed the design to a sheet of paper, even with a transparent background, you cannot make the sheet clear. Does all that make sense?