I have no personal experience with the type of affliction you have, but IMO, there's no reason for cycling shoes to be snug or uncomfortable. Clipless pedals do enable increased pedaling efficiency, but they also restrict your foot to one position (with the possibility of some angular float). Flat pedals allow you to move your foot around to pedal with the ball of the foot, the instep, etc. This may or may not be beneficial with your condition.