So you agree that there's a design motif, but don't see a problem with breaking that motif? Based on your table, seeds and darts wouldn't vary by shape, which is already how they are. If I added shape variance then seeds/darts would also appear in the same cell as stones.

I agree that adding icons is a bit redundant for stones (immediately discernible by shape), in the exact same way it would be redundant for seeds and darts (immediately discernible by color), but there are some cases where it may be helpful for players who have a hard time discerning by color (colorblindness, in the extreme case), and it would be inconsistent to add symbols for seeds/darts and not also for stones.

As for the 'elevated' bit, in general I don't want to add a lot of specific and awkward to explain gameplay interactions like that.