howdy,
yes I totally understand your issue. Unfortunately, from digging into the coding and with my limited knowledge of coding, there is no way to make the gates only “trigger” with a specific collision mask. It appears that the coding is looking for any collision mask operated by the user. I could maybe make an option where you could go around and turn the auto sensor “off” on the crossing gates by lowering the trigger area below the ground? But then you would still have to turn it back on before it would function for the train, which would be the same as just turning it on and off for the train.. I wish I could do more, butt for now I recommend just disabling the animated object extension mod when driving vehicles, and enabling for train driving.