When trying to make operational stops in scenarios, it only lasts 20 seconds. I read recently this was broken in a update a few years ago. The train stops for the desired amount of time you want it to when using AI, but when using your own consist, it's only 10 seconds. It should be fixed to allow the scenario creator to make any train stop for the amount of the time the player wants, say anything from 10 minutes to a hour for example, for both player consist and ai traffic.
Think of the dispatcher a bit more realistic. A train cannot just stop anywhere as long as the driver wants to. If you want a Stop instructions that takes five minutes, activate the clock symbol and make it a timed stop, then you can enter the planned arrival/departure time. That's exactly for your purpose.
I think I'm getting it. This is so by design because it is not a passenger stop. Scenario creators like Not.Silent uses messages to tell the player when to leave in this case. Or use a blocking service that exits the next block on your planned departure. But for the AI it works as I just checked. As this is very much a core thing and would break all scenarios, don't expect it to be changed.