Good point. Meta's brand identity is pretty much the blue you picked. I see your marker color is exactly the hex value for blue that's on most of their website.
I think you could go a little lighter, pretty sure the actual trains have a lighter more saturated blue on them. Something closer to the blue you're using for the Mass Bay Trans Authority would be fine, and there's no overlap in service areas to make that confusing.
Or maybe different marker size/shape for regional vs national trains.