If you mean making the element free to rotate in whatever direction then just click EDIT, go to Model Properties, and uncheck Restrict Rotations.

Hit CTRL+A or click the EDIT tab and hit Select All. Then open your element list, right-click on an element, go to textures and then go to customize.

I use texture atlases to combine all of my textures into one single image. The problem is, I constantly have to rearrange the textures in the image so that the UV box highlights each one symmetrically. I heard that cubik pro has arrow key functionality in the UV editor to position the box where you ...

I vote for this as well.

No I mean without mesh or voxels.

Just a thought. Maybe come triangles, octagons, polygons, etc. Would be much less time consuming.