In MSTS a common way to put a signal at red in front of a player train or AI train is to put after the signal an invisible loco with a very short path and a Waiting point in between. The signal remains red until the invisible loco reaches the waiting point, the waiting point is expired and the end of path is reached.
In some countries like Italy and also Czech Republic and Slovakia for this the so called CD-service invisible engines are very often used (see also this bug https://bugs.launchpad.net/or/+bug/1327578 that I think reports the same problem, although with some linguistic problems). Of course also other invisible engines can be used for this.
I have created and attach here a very small activity with MSTS original rolling stock and based on the standard Marias Pass route.
Running MSTS following can be seen: the player train has to wait about two minutes before starting from Cutbank, because the D9 AI train is waiting at the other part of the signal, and therefore the signal stays at red. When the waiting time expires, the D9 AI train disappears and the player train gets a green signal.
On OR the D9 AI train does not even appear and the player train immediately gets the green signal.