I don't think it's a question of realism, but rather abstraction of ground crew procedures, and understanding of practicality in what is a computer game at the end of the day.
I believe that the real navigation system needs 40 mins to align. However, it is certainly something that the ground crew would set up, and would be done by the planned take-off time.
The best solution would be to give players an alignment "cheat" in Special options tab. This is not unprecedented, as many aircraft have things like simplified crosshair, take-off, nosewheel, etc.
If the Realism cheat is not set up on the server, the navigation system is simply unusable for any precise task, and I think it's less realistic than starting pre-aligned. I imagine the only time when a real pilot would take off without proper alignment is an emergency scramble. Any normal mission, the ground crew would set up the helicopter for planned take-off time.
In, particular, none of the Single Player campaigns that I've played have this enabled. They also plan the take-off time to be immediate. So in practice you just always have extremely poor nav precision. I strongly believe this is way less realistic than having your machine aligned when you load into a mission.
I personally actually enjoy playing with the weakness of the system, and needing to do fixtaking - however, this does no good if you lose alignment in a few minutes after anyway. What I don't enjoy is being expected to wait 20-40 mins before I start the Ka50 up to be able to meaningfully use the system.
Additionally, this is a video game, and you cannot expect people to wait this long. As someone above pointed out, refuel and rearm takes 2 minutes instead of dozens, and you can do it at any position in the airfield vicinity, so a departure from literal realism is not unprecedented here. Having the option to simplify this behavior is reasonable. I would see this as an abstraction of ground procedure.