If I understand you correctly, I think this is more of an Aseprite question than a question about my script. The only thing that my script does in regards to a "transparent colour" is that all of the transparent pixels in your Aseprite image (if any exist) will be converted to the IFF file using the colour index that you've identified as the transparent colour (as shown in the Sprite → Properties window.)
So, for example, if you have set your transparent colour index to #0, and it is black, and your sprite is a simple yellow circle surrounded by transparent pixels, the IFF file exported will be a yellow circle with black pixels all around it. Remember that IFF files don't support alpha channels, so your final IFF file will always be completely opaque.
So all you really need to do in Aseprite, is just draw your sprite on a transparent background and export to an IFF file as normal. That file will not have a transparent background. If you'd rather not draw your sprite on a transparent canvas, and would rather see a solid colour for the canvas instead, then when you create a new Aseprite image, be sure to select "White" or "Black" as the background instead of "Transparent" in the New Sprite window.
Hope that helps!