You've already listed Stalker Call of Pripyat (3rd game of series, has static train engines and cars, train yards, tunnels, tracks crossing thru zones).

Stalker Shadow of Chernobyl (1st of series) also has similar representation of trains as does Stalker Call of Pripyat .

I don't recall if Stalker Clear Sky (2nd in series) does or not.

Signal Ops has multiple levels with trains, including moving trains, a train that crashes and wrecks, and a large train-yard level.

Far Cry 2 has zone-crossing train tracks with static trains, a medium-sized train-yard with multiple missions, several small train-yards and many spurs, a train ambush, and mission involving a large train-bridge over a deep gorge.

I.G.I 2 Covert Strike has an underground train-yard and fighting across moving trains on parallel tracks. Probably other train-related levels that I am forgetting..

I.G.I. 1 I'm Going In (not on GOG) has multiple train and train-yard levels.

Half-Life 2 (not on GOG) has plenty of trains, including a very large train bridge with fast-moving trains that you spend quite some time traversing and "mission-ing".

Stalker Shadow of Chernobyl

Stalker Clear Sky

Signal Ops

Far Cry 2

I.G.I 2 Covert Strike

Offline is a point & click horror exploration game where you are driving a subway train. It's mellow and dreamlike and might swallow your soul.

Review here:
https://www.rockpapershotgun.com/2014/12/11/freeware-garden-off%C9%ADine/

Download here:
https://polclarissou.itch.io/offline

http://train-simulator.com/

I played this and was massively letdown. I was expecting something...better, and more interactive.

Command & Conquer Generals features trains.
I think one of the Red Alert games (possibly the 3rd one) also has trains although I am not 100% sure.
Fallout 3, Fallout New Vegas and Fallout 4 all have trains in them (I believe there are even mods for the games that have trains that work and move)

Two others...

   ▪  <span class="bold">The Raven ­– Legacy of a Master Thief</span>   (GOG)
     Many sequences take place on a train, especially in the first episode.

   ▪  <span class="bold">Ticket to Ride</span>   (Steam)
     PC & Mac adaptations of the board game " Ticket to Ride ".

Stalker is a good one