I made an account just to thank you, this is so sincerely appreciated!
The mods I use are WhyEm's DLC, Rampage Trainer and a mod that unlocks the preorder content and noticed that I was having the issue with trains not spawning and missing passengers in stagecoaches and such. I suppose I am fortunate in that I don't believe I was having any problems with wildlife and the towns and city population were always significant, but there is no question that I was not seeing trains or passengers.
Using this file you've shared to replace the folders in WhyEm's along with the gameconfig mod recommended earlier in this thread, I loaded up a my latest save file (in Epilogue 2) and tested it by first using minimal parts of the mod. So I went to Valentine and stripped all of my guns that had any of WhyEm's carvings or varnishes, deleted all of my saved outfits and made a new outfit for John using the classic hat but I kept his hairstyle provided by WhyEm's along with the Cowboy gloves, and I believe those are the only mod-added items on screen or saved on my horse. I don't really use the horse related items so that wasn't involved at all.
And sure enough, there was a train leaving Valentine station as I approached from the gun shop. I turned around and went to the saloon to eat, then rented a room to skip time to the following morning, and rode out into the Heartlands and when I was over by the ruins of Cornwall's Kerosene and Tar I heard a train moving and saw the smoke way up in the distance and chased after it. After going through the tunnel I caught up to it and there was a guard in the back, and in the passenger cars each one had several people in it! I took a photo which I've attached to this post to show it. I went on to encounter freight trains and passenger trains several times in different parts of the map, and passed countless stagecoaches some of which had up to three passengers besides the driver.
As I tried adding a few more items of clothing from the mod everything still seemed to be working properly, so I wanted to let you know that at least for one person your efforts appear to have made a significant difference. I have yet to really push the boundaries or try it without the gameconfig mod active, but I intend to soon and will share the results afterwards. One issue I did have which I assume should be related to the gameconfig mod is that after about an hour or so of playing I was beginning to get frame rate drops down to 30 FPS and even lower whenever heavy snow or rain appeared, whereas I had gotten everything running at 60 FPS months ago, and this never happened before. I play it on a laptop with a 1660ti attached to a 2550x1440 monitor but with the resolution in-game set to 1980x1080 to maintain the frame rate, so it is not a super powerful setup but certainly can handle the game by putting certain settings at medium.
Another thing, probably not nearly as many people would be interested if they come across this post, but I have the exact same modded setup installed on my Steam Deck and often go back and forth between it and my computer and I also will be trying this out there, and will share my results after. But basically if I can fix the frame rate issue, the other issue will for me be as good as fixed.