The Legacy 360PM manual is wrong, that was discussed here recently by the Lionel folks, specifically Dave Olsen. The only reason they stated that was because the circuit protection on a single transformer would likely trip before the Legacy 360 PM circuit protection. However, that's not a safety or damage issue of any kind. He acknowledged that the "warning" was probably a bit over the top, it should have really been a "by the way" statement just pointing out that fact.
Of course, since we were talking about replacing the standard 180W TMCC PowerMaster with the similar Legacy version, this whole discussion is really moot and not on point. Let's discuss what the OP actually is wanting to do, not drive off into the weeds on a totally different trip.