Interesting. I honestly don't recall ever hearing that keyboard counter melody before. I also have the MT-200 and recorded Passport.mid on it and it doesn't have it either. My guess is there must be a different version of the .mid file out there that doesn't have that included? Although I had an SCB-55 attached to my SB-16 back in the mid 90s and I never heard that keyboard section then either. What firmware version is on your mt-200?
In watching other vids on Youtube it is most definitely supposed to be there? The ONLY thing I can figure is that it isn't an issue with voices. It could be that secondary keyboard is using an instrument that the MT-200 might not actually have? I will have to bring this up later tonight at home if I remember in Midiplayer to see if there are any channels that are kicking off and not actually playing.
Here is my MT-200 playing it directly off the internal diskdrive at around 2:03 mark in the video...
https://youtu.be/ZwPEdGAcuRM?t=123
** UPDATE **
Just got home and fire up a new copy of Passport.mid I got from one of the many YT vids. Ran it through Midiplayer and the missing additional countermelody is present. I then copied it to my Gotek flashdrive and it is still there! So I have to suspect that you and I just happen to have a version of Passport.mid that is missing this counter melody. Check the version in the link below on your MT-200 and see what you get because I'm getting all of the instruments now.
https://www.dropbox.com/s/vrkabhiq4a5xfck/passport.mid?dl=0
Midi Modules: MT-32 (OLD), MT-200, MT-300, MT-90S, MT-90U, SD-20