I seem to remember hearing that that's how it is irl, although honestly they should have split them into part 1 and part 2 so you have the option to go back to the menu and back in so you don't have to wait. Similar to the 150 and 166 services on Riviera that have to wait at Dawlish Warren for a faster 802 or 220 to pass
Answer to the OP is because the timetable has been set up in a rather slapdash manner and we are still awaiting the main fixes.
I seem to remember that a 5 minute wait was added because users were complaining that not enough time was available to set up the systems - something not necessary irl, since they are normally already enabled when the diver takes over.
The standard 90 seconds or so should be more than enough for the average player to set things up. We don’t need 5 minutes. As the loading splash screens tell us, if you want to practice setting up, spawn the loco or unit in Training Centre.
