Those are good points which I haven't included in my theories yet. Well the crystals mentioned in "Mudd's Women" were lithium crystals not dilithium. I don't think we have to throw this away as early series weirdness, the two crystals seem to have too different functions. dilithiums crystals are clearly referred to as the source of the ships power. While in "Mudd's Women" ships power is being feed through the lithium crystals. As far as the shape of the crystal goes that could make "scifi-sense" if the shape the crystals are cut into affects the resonance of the energy inside. Perhaps the only was to get a certain energy to flow out of the crystals is for them to be cut in a shape that allows that certain resonance. So crystals that aren't optimally shaped would have unpredictable output, maybe too much, maybe too little.