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Well spotted, sign of a very good builder when they not only know to check, but also the approx deviation that they come in from the mftr. Suspect for regular road duty the mftr would 'match' the two parts of the block/gearbox casing that have similar mis-alignment, or cancel each others deviation out by careful matching, and then they'd be fine. But under race duty cycle, they'd be issues.
It's how the block has been machined to accept the cam carrier, and the engine builder says 'most of them are like that from factory", which is, erm, not great. But clearly most are fine with it.
Given the increase in load that this one will see this isn't good enough and the engine will come apart again for this to be fixed.