Interestingly, (or not, as the case may be?), we have been dealing with stumps this past week. Mostly very old conifer bushes and because of the amount of material that would need carting away we called in a tree surgeon we know and he got most of the roots out. One was a pyracantha and he cut the stump down as far as he could, drilled holes into it and put some brushwood killer in the holes and capped them. That particular wood is as hard as iron, and he was worried about where the tap roots might meet up with drains and stuff - they seem to run for miles - so played safe. We have covered it in soil and put a stone on the top. I would imagine that if you put in very young plants that don’t need much depth to start with, the roots will soon find their own spaces.