For the same reasons Prince Rupert makes sense, the Alberni terminal makes sense.
Shipping companies don't necessarily care about the logistics on the ground, that's somebody else's job to figure out. They care about the fastest shipping time from Point A to Point B and a terminal in the Alberni Inlet (it wouldn't be all the way up the inlet, it'd be approximately half-way up the inlet) cuts an entire day off their sailing times. That's huge.
I would imagine that the containers will be moved via rail to the Nanaimo area (the rail right-of-way already exists, it just needs proper upgrading which is far cheaper than cutting a new route). From there they would indeed be loaded onto freight barges or freight+rail barges like they use in Alaska (see picture below). There would be enough containers on such a barge to stack an entire CN freight train, if not enough for a second train.
There's also the environmental issue. Fewer massive vessels traversing the straight means fewer disruptions for wildlife and a significantly reduced risk of an incident.