It could be undertorqued too. In that case there would be a lot of
fretting under the base flange of the cylinder, and probably on the
main bearing webs too.

If it hasn't been disassembled yet, you might check the other
throughstuds to see what torque is required to very slightly further
tighten them - giving you an indication of how close to the spec the
previous assembler was.

Another possibility is the hardness of the thru studs I don't know
what the spec is (probably not published ) but maybe Rockwell C = 48 to
52 or so?

That engine wouldn't have gone much further at all. You were lucky.