Have just read that going west to east is better route for scenic reasons. Think you see more of the mountains during the day and sleep through the plains at night ?
Glacier National Park is the true highlight of this train trip, (followed by the Columbia River and Gorge) so I would be determining which way to travel, how long to get off for, and whether to rent a vehicle, based on best use of the park.
So there's a choice between arriving into West Glacier early morning or late evening. There might be the option of getting off on one side of the park and getting back on on the other side, and so on. Personally I think the park and environs warrant three nights ... just need to think through the logistics.