OK, great conversation but let's look at this a little closer.
The first scenario is that this generator just happens to output the 208 high leg on the C phase. This is a good time to question the electrician who is changing the ATS and ask if he checked phase rotation and if he verified that the high leg was indeed coming off of the C phase.
Scenario two is possible that the electrician did verify that this generator high leg does come off the C phase so he marked it appropriately and THEN he placed it on th B phase in the ATS to match what was done before and phase rotation.
Another scenario is that, well, the electrician's helper simply does not know and just marked the wrong wire as the high leg. Either way, when doing this inspection, you will have to ask a lot of questions.
However, what phase a generator produces the high-leg is not covered by the code, where it lands on a bus is certainly relevant.
Thoughts?