trains' advantage on cds is intended, imho, and i would not really like to see that changed, cause trains could not b used anymore then, especially against agressive npcs.
u cannot stop a train from behind while it's in a cruise, if it has no containers, since u have nothing to hit from behind except containers' carrier, and that one has little to do with engines, which r up front. so, a train with no containers is usually hard to target with cms, since u must hit cockpit (usually impossible from behind). the same goes for guns too, and imho, it's perfectly normal that way and should not b changed.
u still can stop it with cd guns, anyway, if u really need that. also mosquito missiles usually stop it too, because of their speed, but it depends upon place of hit.