Not to get too excited about DCR calculators, these things are black boxes inside of which we have no idea what's really going on. The simplistic approach is to say that because of reverse pumping, some portion of the intake mixture is being pushed by the piston back into the intake track and out the carb. Hence mixture stand off for this and other reasons. And they pontificate that this is somehow proportional to when the intake valve closes. Therefore, the mixture density in the cylinder is reduced by some fraction of less than what could be obtained if the cylinder could/would breath till it was full of mixture at atmospheric pressure. Then the density, or pressure, would simply be the SCR times atmospheric pressure and the Dynamic Compression Pressure Ratio would be equal to the Static Mechanical Compression Ratio.
However, and it's a big "however"! The SCR is as dependent upon RPM, perhaps more-so than just when the intake valve closes. This is because the incoming mixture has mass and velocity. Mass times the velocity gives an inertial weight to mixture. At low RPMs this inertial weigh is low and the rising piston can easily push the incoming charge backwards, a condition that would be accentuated by a late closing valve resulting in the DCR being less than the SCR in terms of pressure. But as the RPMs increase, so does the velocity of the mixture and times its mass the mixture begins to get rather, shall we say, porky. There is a point in rising revs where it resists being pumped out of the cylinder and will in fact continue to rush into the diminishing volume of the cylinder against the efforts of the rising piston. At this point the density in the cylinder is increasing and therefore the DCR is going up. On top of this general effect with increasing RPM, the velocity in the intake system is also controlled by the size/volume of the ports, valves, plenum volume and carb size as well as RPMs. So one can see that these one size fits all calculators are either missing the ability to be sensitive to a lot of missing information about your engine, or are making some pretty substantial assumptions about it.
As far as clearance to the quench deck is concerned, don't loose track of the fact that going over TDC on the exhaust stroke, the inertia of the piston and rod will take up all the rod clearance and that has to be added to the length of the piston and rod assembly which is eating away your safety margin keeping piston crown and head deck separated. Also, the piston is twisting sideways as it takes up the thrust clearance of the skirt, thus allowing a side of the crown to come closer to the head. This is not to even take in consideration for things stretching from inertia or the formation of hard deposits on the top of the piston and bottom of the head. You need to be sure to provide structural clearance for which with a steel rod and nominal production clearances .040 inch is considered to be minimally adequate. You can buy a lot of gasoline for what it costs to fix a collision between the piston and the head.