Yepp, in this case it maybe the whatever ;) I cannot specify it because I use and hear "metróállomás" significantly more often, therefore I don't know who use the "metrómegálló" form. But both are correct and this is highly probably that you're right with that reason. It's a strange thing, even funny :D I say let's accept both (and let poor newbies desperately memorize those five-syllable words... Take my sympathy, good fellows :D )
I think the main question here is: does English use "stop" on its own (without "bus", "tram", whatever) to refer to a designated stopping place of a public transport vehicle? Because Hungarian does. "Megálló" is literally "(a) stopping (place)", and is frequently used without any qualifier. As in "where is the stop?", "I'll wait for you at the stop", "two stops from here", etc.
I think the default usage (without a qualifier) is for a surface transportation line (bus, tram, trolley bus) simply because those are the most numerous. But it can certainly refer to a few other modes of transportation, as well.