The main difference and the reason Makuta do not “trully” control elements outside of shadow is that their other abilities are non-elemental, meaning they draw from their physical energy, not elemental energy.
The practical result is that the range of applications for powers like plasma or vacuum is much narrower than a level of control a Toa would have.
I am actually planning a bigger analysis topic detailing the many different kinds of energies used by the characters within story and their properties/differences.
Also it should be mentioned that when Makuta was controling the environment of the island, he was not doing so using his kraata powers, but by accessing and manipulating the GSR camouflage systems.
EDIT: It’s out: Many flavors of energy in the Matoran Universe