That strong horseshoe shape in the most kinky root probably marks the point where that seed germinated at or barely below the surface and subsequent heavy rain events would have washed the soil out in stages. I have many potted JM's with weird root structures at the soil level and it has never been an issue. Also, as you said the plant location was alongside the house, it might be worth observing the area during heavy rain to see if receives excess runoff from the roof or gutters - it might be something like that has washed the soil out. Very healthy looking seedlings in any case and the red stems are lovely!
