Ian. Yes, some engine blocks were apparently the basis for either being machined as a 292 OR a 312. The determiner of their final use in production was the main caps used in '56, '57, '58, '59, and '60, - the years of regular production of the 312. Those engine block castings to be completed as 292s had main caps marked EBU while 312s had main caps marked ECZ. Additionally...
Per JM's chart, my expectation is that these particular engine blocks [ ECZ-A, ECZ-B, ECZ-C, EDB-E, and B9AE-F ] used the same sand cores when they were cast to be used as 292 or 312 cores. I speculate that other '50s y-blocks may have had different sand cores used in the sand casting process because of their being used to form cylinder thicknesses for the smaller finished bore size of the 239, 256, 272, or 292-only engines.
In addition to main bearing bore size and the bearing tang location, the 312 caps were physically taller and required longer bolts. Longer bolts because of the increased 312 cap height, not because of a difference in how far the bolts screwed into the engine block depth.
Sooo... I know that Ted Eaton has bored '60s blocks to 3.859 for the Engine Master's Competition after carefully sonic testing the blocks for core shift and rejecting some because of it. Remember that Ford only supplied a maximum oversize piston size of .040 for the 312.
In a long standing entry on John Mummert's web site in the Technical section titled Parts to Look For, top of the page sub titled Blocks, John made the statement:
292 blocks from 55-64 are fairly easy to find. Slight improvements were made in 1959 with deeper drilled main cap threads. 61-64 C1AE and C2AE blocks have additional material in the main webs. These blocks typically don't sonic test as thick as earlier blocks. Therefore if a good early block is found drill and tap the main cap threads deeper and use the early block. Base your decision on cylinder wall thickness over added material in main webs.
312 blocks have the advantage of use of 312 crankshaft without modification. The down side is 312 blocks are difficult to find, expensive and have often been bored .040' or .060"oversize. These block typically sonic test thin at these bore sizes. 312 blocks are often cracked near the main cap bolt holes.
NoShortcuts
a.k.a. Charlie Brown
near Syracuse, New York