Dr, You raise an interesting point.
When my '67 XR7GT Cougar was a few months old, I acquired a '63 427 engine, in a basket, and set about putting it together to go in the 'Cat'. I won't go through all the parts, but I put in such things as a new 'AA' cam and a set of shell lifters, did a valve job, and topped it all off with an 'XE' Sidewinder. I cut the flanges off a set of Hooker (I think) headers and substituted a set of up-'n'-down-only '27 pieces, etc.
When it came time to put the engine in the car, I noticed the mis-match at the mounts and got all excited for a few minutes. But even the two on the block and 3 on the '67 mounts lined-up OK somehow and the engine dropped right down where it was supposed to go.
I don't remember all the details, but somehow it DID fit together without any problems. I've noticed other comments such as yours, but I know what I did!
??
KS