Yes, If you want to have homgenous groups of same units, you need each to contain, and occupy a circle. The collision are always made with bounding circles (because units rotate on themselves) so with none circular design, you will have different spaces between units.
That's why the SC2 siege tank has additionnal tracks on its side.
For more unique units, like in command and conquer, you can make differently.
Could you make a screen with more light, and an isometric camera? The shininess of the material is important to get more contrast between facets.
Nice work !