Umm.. he said the engine was pretty much straight on, not angled right OR left.
And, he could have installed the firewall wrong which could account for the difference in offset. Brett, I don't understand what you mean by backwards running engine. If it's mounted wrong, well, it's mounted wrong. Has nothing do do with the way the prop turns.
But, as you also said, it probably won't make much difference in a trainer. It is probably ok to fly the way it is without making any changes or adjustments. But, if you really gotta get the thrust angle right, insert a washer or two to push it to the right a bit (standing from behind that is..

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CGr