When we went on the White pass last year I think it was $93 per adult booked on Princess. It was about $10 difference last year booking at station vs. boat, not $40 difference. The train did drop us off at the station on its return to Skagway so we could walk around town.
I have attached the schedule website for you to compare to onboard booking.
It was worth everypenny I spent for the trip. Look at photos of our trip in the photo gallery.