These days most engines have a barcode stuck on at the beginning of the assembly process, this is read as it moves and ensures the right parts are installed.

In cases where an engine is being supplied as in this case, the dealer may record this on the system to tie it to the 'original' number stamped, perhaps?

I don't doubt the veracity of that statement but if engines leave factory w/out a number how do recalls and updates get dealt with?

Not quite sure what that means but I can tell you its 100% correct. Said it on here before but when I bought a brand new crate 2 litre Zetec for my "classic" it came with no number on it. Asked the supplier what i should do and he explained that it was intended that you stamp the old number onto the new engine. The Ford VIN actually includes the engine number in the code, if the engine number were to change theoretically the VIN would need changing and what a nightmage that would be.

The engine has a barcode sticker on the front and that number may well get cross referenced with your reg on Fords computer to deal with recalls and updates. In my case that was irelevant, think the warranty ended the moment I got the engine home and stripped all the redundant bits off it.