It's not the bottom of the foot. In fact, I am well-acquainted with plantar fasciitis; my wife has it. My pain is on the top/side of the foot at the instep.
Sounds like the anterior talofibular ligament, or it's attachments. (eg, http://kicksnet.com/ankle-foot-anatomy/
) That's a relatively small ligament [ligaments connect bones to bones] in your foot which can be bothered by the point-your-toes motion (dorsiflexion) combined with the angle-your-toes-towards-each-other motion (adduction). ie, exactly what you do when you sit in seiza. When you see your doctor, be sure to describe the exact "contortion" -- which is what he'll probably call it
-- of seiza.
My experience has been that the more your "crush" your heels outward with the pressure of your butt, the more you torment that ligament. In seiza, rotating your heels towards each other (or upwards and inwards) will decrease the load on that ligament -- but at the expense of requiring your ankle to point your toes further (reduce adduction, increase dorsiflexion).
I also suggest paying attention to your knee joints. Your knee should be acting as a simple hinge. Do not position your shins under your thighs so that the thigh falls inward nor outward; that loads your knee oddly, which can put a twisting force into your lower leg that "appears" as pain down in your ankle joint where that ligament transfers it from your fibular to the talus.