I'm struggling with realism, when design my own scenarios.
And it's very annoying, when something in the game dictate you to behave such way, which is un-prototypical and unnatural for railroad operation.
First, default track markers (destination markers, platform markers) on some routes.
They are too short, or too close to signal, or often both. Short markers may fail to trigger event in scenario, leaving scenario in "not passed" state. Example - gooddamn Browning station in Marias Pass, which always fail to trigger.
Markers located too close to signal, require you to stop in non-natural way.
I believe neither railroad in the world requires you to stop like that (beside some subway or urban commuter rail systems). It's just too unsafe. Rules in some countries require the opposite thing - stop at least 100m (or 90 yds for US friends) from red signal. That's a safety "margin" in case if train has increased stopping distance due to it's heavy weight or insufficient brakes.

Also, there is often road crossing in the station, before signal. It's quite common that train stops before the intersection, not after. Imagine, if train stops for 20 minutes, and ambulance need to go to the other side. Pretty obvious reason to stay away from level crossing.
Good option is to allow our engineer to stop where (s)he wants before the signal, but allowing a better choice.

Here is a rescue custom scenario markers.
Go to infrastructure (semaphore icon), choose "Marker - destination"

Place the marker and stretch it , using creen marks on the end.
I make it wide enough, so engineer in the game do not need driving aids (HUD) to calculate precise stop location. Just stop, using common sense, in the signal visibility.

Don't forget to rename it to some meaningful name

Another annoying thing - is when scenario requires mandatory stop, even if there is a green light.
It happens, when it was red, you reduced speed, opposite train already cleared the signal and it changed to green.
but in the scenario task list there is still mandatory stop, which needs to be triggered for success.
To make stop optional, set min speed 1 MPH .

I do this for every meet point, with exclusion of end points.
I also planning tutorial on using sound markers to trigger talking detectors in Stevens Pass (if there isn't any already)