Frames of reference matter. Whether the train or the people moving happened it doesnt matter to the portal. There is net movement and the momentum is the mass of the person moving x the speed of the train.
Imagine the train was moving the speed of light. If the person exiting the other end of the portal wasnt coming out at the speed of light their body would come out like a soup. All the atoms in their body compressing to escape at some randomly low speed… actually it might make a tiny black hole on the other end as the atoms compress infinitely.