You might give us a little more info about why your asking the question in order for us to narrow our answers. Are you trying to put a crate engine (motors are electric, btw) into a classic Ford and pass it off as original? Are you trying to identify whether or not an engine is a crate because the owner of a car your looking at said he put a crate engine in the car? Are you wanting to purchase a crate engine to put in a classic Ford you already own instead of rebuilding the engine you have, or replacing the one your missing?
A Ford crate engine will have much later casting numbers on it, to me, a crate engine is built from all new parts, are you talking about a rebuilt engine using a seasoned block and everything else new?
The things that would possibly be different in my mind are:
1. Engine mount boss location, quantity. As an example, the early FE blocks are different than the later blocks where they added a boss.
2. Water pump and timing cover. As an example, the later model 302's have a different timing cover (no dipstick tube location) and the water pump is configured differently (outlet on opposite side).
3. Accessory holes on the heads. I'm guessing most BBF crate engines probably have aluminum heads.
4. Exhaust ports & bolt hole locations. Although I doubt anyone uses them on a crate engine, some of the good Ford BB aluminum heads have BBC bolt pattern and port openings.