I don't know why but I've developed a pet peeve for this. Would you not agree that Castle Story more resembles Dwarf Fortress than Minecraft? Therefore why do we not refer to it as a Dwarf Fortress clone. DF had the idea of blocks long before Minecraft. Unless there is more to it than that.
I'll have to admit to not having a clue about where Notch hopes to derive the fun from 0x10c, nor to understanding entirely the premise, but again the only reference I can find to Minecraft is the distribution style.
I just find it a bit derogatory to label such indie titles as 'clones'.