Having lived in SE Alaska for 25 years I have had my share of time on the Alaska Marine Hwy System. I would never try this in the summer. However the smaller your vehicle the greater your chance of being able to pull this off but expect delays. Each departure you're required to check in by a specific time at the departure terminal. If you fail to check in by that time you are pulled off the voyage manifest and placed on a wait list and someone ahead of you who is at the terminal above you on the wait list will get your deck space if their vehicle will fit. They do a lot of picking and choosing.
Summer of 2016 we hopped from Skagway to Haines with our full size F-550 and a 31 foot 5th wheel trailer. We had reservations. Vehicles were plucked out of the waiting area (lines by destination) and the deck crews direct them onto the vehicle deck. The final spot was across the bow. The ferries load from the front right of the hull except in Bellingham. The last vehicle was a 45' Class A coach which had to back down the steep loading ramp (tide was out) and when parked was sitting bow door to bow door cross ways but the vessel was full when we departed Skagway.
To disembark we had to back the length of the vessel as we were loaded front in near the stern. The deck crew was very helpful with one crew member standing outside the drivers window directing me on the manuver. With his help I was able to back the length of the ship and then jack knife the trailer to the port side of the vessel then exit out the starbard side up the ramp to the Haines terminal and beyond. That is only a one hour voyage but takes 4-5 hrs by the time you check in on time, wait, vessel is unloaded, you load, travel then are systematically unloaded at the destination port. Vehicles are all loaded depending on their destination port of call.
I have never traveled on the BC inner coastal ferry system so I can't speak to that.
I can report that the Alaska Marine Hwy Ferry crews are very well trained. I have been aboard sailings a hand full of times when rescues were made or a passenger was e-vac'ed off for medical reasons to a higher level of care. They run regular muster drills for the crews as required by the USCG to stay proficient with fire drills, high speed rescue boat (hard bottom inflatable) operations so when duty calls they are ready to answer the call.
Most of the vessels in their fleet are getting OLD. So breakdowns do occur or additional problems are discovered during their major yearly maintenance lay ups which muckers up and delays the ships working their sailing schedules which can be a real pain if you are traveling on any type of time line to or from Alaska.
2006 F-550, Crew cab, 4x4 w/factory bed getting 12 mpg @ 50,000 miles
2006 Lance 1191
2006 Wells Cargo 14' Cycle Wagon
2017 Grand Design 5th wheel with EezTire TPMS
2017 F-450 4x4 crew cab King Ranch