Gaming

There is a game in development that does some of this stuff. It's called Junxtions I think. Looked interesting

Rail Route does not tick all the boxes and is higher level, but the signalling and shared track mechanisms are done quite well.

I liked factory town; the trains need to stop and stations to unload and refuel, and they only go one direction. Its somewhat simplified but satisfying.

Probably not you are searching, but I love openttd

Satisfactory has quite the satisfactory railway mechanics: in addition to what you say what you want with them, you also have to place proper semaphores in order not to have them crashing each other.

Efficient networks require roundabouts and double one-way tracks, but sometimes it's much more convenient to either have maze-like single one-way tracks (makes paths longer) or two-way tracks (blocks traffic, and gets worse the longer it is).

... there is no "intellgence" with vehicle paths, though: trucks and trains always pick the shortest path, and if they've gotta wait, they're gonna wait (unless you screw up the semaphores, in which case kaboom).

I love engineering games like that but I don't believe any game will check all the boxes you want.

Like others here I vouch for Satisfactory Trucks and especially the Railways. You can go quite deep there if you want. Drones do the clipping and are bit too easy so skip them.

While not what you exactly wished I'd say give Transport Tycoon or rather OpenTTD a go. While not as pedantic with traffic as you hope you will have a blast of a time doing beautifully orchestrated trains, airports, ferries and trucks/busses and optimizing the routes from resources to consumers.

And to reiterate. I don't believe a game exists that matches most of your wishes. I hope it will eventually!

maybe open ttd which was free before but has now been rolled into transport tycoon (of which it was basically a clone/fork but with many more years of development by now, so not meant derogatory):

https://www.openttd.org/
https://store.steampowered.com/app/3766810/Transport_Tycoon_Deluxe/ (also on gog)

This isn't helpful, but I was actually really disappointed by the people aspect of workers and resources. There's no agent model with people picking routes to their workplace or needs. They're just another type of resource you shunt around with limited models of searching from transit stops.

But yeah as far as trains are concerned factorio does seem to be the best available.

Transport Fever 3 might do some of this stuff. The pedestrians and traffic were quite good in Transport Fever 2 but that one had the train issue you talked about