In Skagway if take the train it has to be thru the cruise line. Trains are usually assigned to certain ships and don't have room for others.
In Juneau & Ketchitcan you can take any tour can buy most tours on the dock.
The only possible issue is that your private tour is late for the ship you need to pay to get to next port. Usually the ship will wait if a ship tour is late.
SS Ithaca , Volendam , Mariner of the Seas (x2) , Veendam , Coral Princess , Island Princess (x3) , Emerald Princess,Sapphire Sapphire (x3),Diamond Princess