Dick,
It's an outlier for sure, but I've seen it. In fact I rented a building with that configuration once in Seattle, it was a PITA because of some of the issues you mentioned. Ours was an open delta to boot, so there were two different transformers on the pole, a 480 secondary single phase and a 480/240 secondary single phase, so in our case, A was the high leg, because the single voltage transformer was connected A-B, the split phase was B to C. So phase to phase was 480V, B or C to neutral was 240V and A to Neutral (or ground) was 415V and thereby unusable. It had been special ordered by a previous tenant who was making printed circuit boards. All we could imagine was that maybe they needed a lot of 240V single phase power for something and didn't want two transformers. Otherwise you're right, it makes little sense.
We ended up calling the utility and having them swap it out for a standard 480/277Y transformer. They did it, then wanted to know if we wanted to keep the old transformers there "just in case", because they were not their standard and had no use for them. We said sure, then after they left we sold them for scrap ;-)
But back to the OP, yes, it is supposed to be marked orange per NEC 110.15, which doesn't specify any voltage; "only the conductor or bus bar having the higher phase voltage to ground shall be durably and permanently marked by an outer finish that is orange in color or by other effective means". However there are some jurisdictions in which local codes have modified that because of pre-existing standards they had prior to 2002. So purple is another color I have seen used.
Lastly, power utilities often have their own standards and they are not required to follow the NEC, which confuses a lot of people. The NEC has to do with how it is marked AFTER the service entrance.