In my experience padmasana is a solid pose for traditional pranayama such as Iyengar style but that when doing Chin pump and kechar he body should be looser and allowed more internal flowing movement so siddhasana allows this. I too have found that siddhasana needs more fine adjustments and that for some people using the heel or end of the extremity as the reference point for adjustment can distort the spine. I have particularly long shins for example so that to sit in a balanced way my heel should be past the center point and touching the opposite thigh. Once I realized that the pose became much more comfortable and balanced. a small rolled up sock to sit on may help but in ,y case does not feel necessary as much as the feeling of getting the legs out of the way of interfering with the balanced seat of the pose much in the way that I don’t want my hands in a fixed position but allowed to rest where is most comfortable. The key here seems to be creating a seat where there is no distracting sensations to interrupt the energy flow through the spine during practice.