Most all cruiseline combo trips are in buses, not vans. The one way train and Yukon option is a good one. The train does NOT get into the Yukon 20 miles short in BC. So if your priority is to enter and say you've been there, this is your only chance.

With a ONE way train - vitally important is your seating, from Skagway sit on the left side facing the engine, from White Pass sit on the right.
The train can fill up, but with a long port day- and flexability you should be able to get a seat if you head straight there and be prepared for the 8:30am train if the rest of the day is sold out.