We only use carry-on luggage for all of our cruises (airlines lost our luggage one time and we swore
never again), but PP can handle yours. Check the Pan Pacific web site
https://www.panpacific.com/en/hotels-and-resorts/pp-vancouver/offers/alaska-cruise-package.html . We got a great rate, free breakfast, wifi, and transfer (but didn't use it) as part of a special "cruise package".
Yes there is about as much walking as PC (from down stairs security to up stairs, cattle-run lines, security, waiting area, hike up the gangway, and into the ship) plus one more line for customs.
Use the hotel transfer for luggage in your case. It's just the same as dropping it off at PC with the luggage handlers: thrown in a huge pile, loaded into the ship and distributed like everyone else some time around dinner at your stateroom door. I don't know how they treat the checked luggage for security and customs.
They really keep the lines moving so there was hardly any standing around waiting.