Red gel would be to increase contrast (soft contrast is often a problem with unbaffled pinhole cameras, because the extremely wide coverage of the pinhole leads to light scattering from the inside of the camera and veiling the image). Clear gel is probably just to have a filler the same thickness so something will clamp evenly. But red gel would also imply a 2- or 3-stop filter factor -- presumably taken into account in the exposure recommendations they give -- and wouldn't be appropriate for all lighting or situations (or films, come to that -- if you mount a 4x5 back in place of the Polaroid, or have the 4x5 camera, and use Efke 25 with a red gel, you'll have, instead of 2 or 3 stops, more like 6 stops filter factor...).