One issue with odd tubers I've found is they decay 2-3x faster than soil. So if you're using a metal shovel, letting soil fall, the tubers often vanish before/as you're picking up the soil. Not sure if that is intended, or a bug.
I have leveled a lot of land with odd tubers in inventory and have never had them used.
I haven't gotten an odd tuber from leveling where soil is used instead of gathered, but I have very little of those areas left.