Sorry for the late reply.
This is not related to Substrate as far as I know. This is a limitation of grooms. The Custom depth value are not rendered with the same anti-aliasing techniques as for the hair samples/color. You can try to offset the hair depth (with a multiply) to get rid off the incorrect depth test in your post process material. This won’t solve your flickering issue in the pixelate pass, as the value won’t be fully stable for the same reason I suppose.
/Charles.