Huh! You seem to have stumbled across something pretty special here, kid! The developers must surely have no explanation for such an arbitrary decision. Truly a mystery we might never be able to solve...
The developers have never commented on this topic, so you will never receive a definitive answer to your question. However, given Moltres is a Fire-type, you would agree Mt. Ember sounds a more fitting location than Victory Road for its encounter, yes?
In the original Red and Blue, both Articuno and Zapdos are encountered in locations fit to their typings, at the Seafoam Islands and Power Plant respectively. It makes sense the developers responded to the opportunity to bring Moltres in line with the others when a more suitable location was added.
(In case this was not apparent, One Island did not exist in Red and Blue, so they could not have put Moltres there in the original games.)
