A bit late to the party, . . . but I'll add a little more to this topic
Mismatch on the intake port is not necessarily a bad thing.
Have you considered it's effect on fuel atomization? = (gas mileage)
What about it's effect on intake port reversion?

Looking at a AT1 / CT1 engine, I've noted that the venturi of the carburetor is 24mm and tapers out to 25mm where it mounts.
Then the cylinder port opening itself is 27.5mm . . . so a mismatch of at least 1.25mm even when perfectly centered . . . and more, if not.
Seems, at least to some extent, "some" mismatch could be partly by design, but I can't prove it.

In most cases, I think a mismatched intake on a high rpm "race bike" , could have less favorable results.

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Thank you Enduronut for chiming in on this! I was really kind of hoping for your and others' insight. Since both pedalcazy and my cylinders seem to be the same on this point I am thinking this was just how things were at that point on the assembly line. Whenever it might have been noticed and whenever a correction was made (and apparently it was, looking at later cylinders online) we would need someone with deeper knowledge of the process there at that time.