By placing the tip too close, you rip this off exposing the sand, stone, and cement mixture that makes up the floor. You can still stain the floor without any problems, but that “cream coat” is what gives the floor personality as it has variations in color, density, and texture that are the result of the trowel or broom finish.
However if you don’t strip off all the cream coat then you are going to get random blotches all over. Obviously it’s just better not to go so hard in the cleaning phase.