>>I recommend booking the rail trip through the shore excursion desk because the railroad sometimes operates as many as sixteen trains at once. If your ship's train gets delayed by congestion, the ship will wait for its return. If you are on another train that gets delayed by congestion, you could miss your ship. <<
This often-stated reason to book on the ship is an "Urban Legend". No ship has ever left Skagway without passengers who were on a WP&YR train. There is only one track - any delay on the line makes everyone late, and that is extremely rare (usually a rockslide, every few years). The advantage "can be" because if you book on the ship, you board at your ship, if not you board 2-4 blocks away - handy for those with mobility issues.