The 18 is part of the serial as used by Ford...it is occasionally not used on the frame front, and I think is never on the two numbers father back. This has parallels in modern number...cars with the modern numbers frequently use the serial only on the secondary stampings, with all the prefixes only on the main tag.
Ford considered the number on the bellhousing the primary number, frame stampings, even the main one up front, were secondary and went on the car only when the factory serialed engine to be used arrived at the frame.
I think the reason it could be left off is that there was no possibility of confusion on any '32-48 type Ford...In some years, there were ONLY Model 18s, in the years with other engines, like 1940, the sequence numbers were very radically different (by many millions) and so the car could not possibly have a 99 or 54 model number with the given serial. I hope you have original trans...that is most convincing thing. But if you have '40 Ford #Xmillion, no other '40 could have that number.