Three docks, and the train comes to two of them
Skagway's cruise berths are the Railroad Dock, the Broadway Dock and the Ore Dock. The Railroad Dock is the long one - over 2,000 feet, enough for two large ships - and the White Pass and Yukon Route has track right on it. At the Broadway Dock the train boards at the landward end of the pier. The Ore Dock was a bulk-carrier berth converted for cruise use, and the railway lists no on-dock boarding there.
The Railroad Dock sits under a mountainside that has dropped rock onto it, and after a 2022 slide it reopened with limits on where gangways could be placed. So if you booked the train expecting to step from ship to carriage, confirm your berth first.
Bring the passport if you're going over the pass
Any excursion that continues past the summit into Canada - to Fraser, Carcross or Whitehorse - crosses the border, and the cruise lines enforce the document rules hard. Carnival's Yukon tour, for example, requires a valid passport for anyone 16 and over, or a passport card, NEXUS card or enhanced driver's licence; it specifically refuses ordinary driver's licences, Real ID, cruise cards, Global Entry cards and expired passports.
Under-16s can use a birth certificate with a raised seal plus photo ID, and a child travelling without both parents needs a letter from the absent parent. Some nationalities also need a Canadian visitor visa. Check all of this before you leave the ship, not at the coach door.
Sources: wpyr.com, khns.org, carnival.com