Well, sideways or rather upright (possibly in a seating position) is probably better but seems not very aerodynamic. I think those are the three possible orientations. But I mean are we seriously considering a transportation system where part of the journey is a black out/red out? The time gain by accelerating with 5g instead of 1g can't be that big (Maybe a few minutes at most?).
Edit: I'm not sure if there's an error in my calculations but with 1g acceleration it should take about 25s to get to 900km/h? That seems ok.
I agree with your calculations, but with an 1g acceleration for 25s, the train will travel a bit more than 3km, and getting to the end of the track (which is 3km according to the article) at close to 900km/h is unlikely to lead to a happy outcome.
If my math is right, in order to accelerate to 900km/h and decelerate to a stop again, all on a 3km track, requires acceleration/deceleration of a bit more than 2g.
Edit: I'm not sure if there's an error in my calculations but with 1g acceleration it should take about 25s to get to 900km/h? That seems ok.