Thank you for your question.
The output GIF will not have transparency or transparent color.
You will need to add transparent color to the output GIF in a different way.
There is no function to output sprite sheets in PNG format.
This tool is not a tool for editing sprite sheets in the first place, so I don't think you will need it. (This tool loads your own sprite sheet, creates animations, shoots them, or applies them to other pico8 projects.)