Sooo, we can mine rocks with the mining laser but can't mine minerals deposits sitting right on the surface.
And we can mine mineral deposits with the terrain manipulator but can't manipulate the terrain i.e. to flatten, lower or raise it...oookkaaay.
Are you listening Hello Games?? (I want to flatten some land for my base).
Always been that way. Use base parts to flatten the ground. Just beware that you might hit the terrain limit which you can only reset on PC.