Let me see if my explanation skills are working. I might exaggerate a bit to make the point.
With the front of the base secured there was no gap under the Front of the base but the rear of the base stuck up .005".
I could tighten the rear screws and it would pull the base down tight in the rear. But, in doing so, technically you are flexing or distorting the rail .005" to close that gap.
If the mount was tightened down it would squeeze nearly all of the compound out and would be bedded in with the five thousandths distortion.
By by leaving the rear of the base loose you have not induced the stress in the base. Once the "bedding compound" sets under that .005" gap you no longer have a gap. So, when you tighten it down, since their is no gap there is no distortion to the base.