This is probably most easily fixed by fixing another aspect of trains, being that they decelerate much too slowly.
Yes, in real life trains are heavy and take a long time to speed up and slow down. Bu in real life freight trains move materials dozens or hundreds of kilometers.
That is not the case in satisfactory. Stations are going to be 1, maybe 2 km apart at most. Sure, you can put stations further apart than this. But if you do, then you're running conveyor belts a LONG way from the various deposits to converge them at the stations, at which point you might as well just run the conveyors all the way to your main base and forget the train entirely.
Take, for example, a route down the left hand edge of the map, as drawn in this image with a blue line. The yellow crossbars represent "obvious" places to put stops.
https://imgur.com/T1YR6uK
But if you actually put stops there, the train can barely get to 30% of its maximum speed if you want to be able to slow down in time for each stop.
Alternatively, you could put just two stops in - one at each end, say - instead of 4. But if you do this, you're running belts half way, even up to 2/3rds of the way, along the route. Ie, you have to consolidate the oil groupwith the north group, and you have to consolidate the two bottom resource groups. So why bother with the train?
This game is not the same as reality, distances between useful stops are much shorter. Therefore in order that trains be useful, they need to be able to start and stop more quickly.
This would therefore also help solve the "not stopping in time for the station" issue.