I just checked, it is indeed easy enough to just hack the JS output and swap the colors for the desired jam colors.
For pico-8 devs who are interested - after exporting to html, open the generated javascript file. The pico-8 color palette is stored as RGB values, comma separated, no spaces. If you want to replace RED (index 8) with another color, just search for "255,0,77" and then swap these with your new desired RGB.
Thanks!