Make the game as normal in PICO-8 and change the colors manually for the HTML export that you submit to the jam.

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.

Big thanks to Tobias V. Langhoff and PaloBlancoGames for sharing how Pico-8 Devs can participate with the required palettes!