When a new Model A cylinder block was machined, the first machine operation was to machine the pan rail and main bearing bolt holes. During this first machine operation the front main bolt and rear main bolt holes on the side opposite to the camshaft were reamed for future machine operations. The drawing note for these two holes reads ".505 ream 1/2 deep for locating machining".
What this does is to establish a plane and 2 locating holes for subsequent machine operations.
The other 5 planes of the cylinder block were machined on at least 5 other special machines.
When a cylinder block was loaded into one of these other machines, the first plane and 2 reamed main bolt holes is where the cylinder block was mated to the machine.
The result was a cylinder block with all machined surfaces flat, square, perpendicular to each other, and in the same location for all cylinder blocks.
Over time (90 years), most engines have been rebuilt several times, and worn surfaces have been machined to make them flat.
The problem with rebuilt engines is that the machinery used to rebuild them does not index on the first plane and 2 reamed main bolt holes, but instead indexes on other features that may be out of location due to previous rebuilds.
A cylinder boring machine is a good example. Most cylinder boring machines use the top surface of the cylinder block as a plane, and determine location of where to bore from indexing low in the cylinder where the rings don't ride. If the top surface is not parallel to the pan rail and/or the cylinders were miss located in a previous rebuild, the engine will not be right.