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.)
Thanks for the quick reply. The use case I was imagining was to create sprite parts in separate software, load them into this software, create animations by moving the parts, then export as GIF/PNG with transparency to use in another game engine.
