Perhaps someone else can answer about the Alaska cruises, but I know that I am paying $5 per person each way for the bus transfers to and from the Grand Princess to the Ft. Lauderdale Airport with the Seabird Air Program. In the past, these transfers used to be included with the air/sea packages. Now, like so many other things, the cruise lines are starting to charge for any extras. I still think it's a good value and very convenient.
Only nine days til cruise number nine... Bob "MacTarheel"
To answer your question about screwing up use of the transfers - nothing should get screwed up if you take the flights that Princess booked for you. That way they know when you are coming/going and send a rep out to meet you.
We just returned from a Southern Carribean aboard the Ocean Princess. We arrived a day early in San Juan, using the Princess air option-also used a hotel in the Princess booklet. All the transfers were included. We were met at the airport by Princess reps, transported to our hotel. The night before embarkation, we were asked to leave our luggage outside out hotel room for pickup (all but carry on). On our embarkation day, they had a Princess rep at the hotel to direct us to a waiting bus, which transported us to the ship. Again, when we debarked, we were directed to waiting buses, which transported us to the airport. Trucks were there to tag and pick up the luggage-this was done by airline. All in all, everything went very smoothly. The coupons for your transfers come as a tear off in your Princess ticket booklet that is part of your cruise docs. Don't know if Alaska will work the same way, but assume it should.
Princess no longer bundles transfers with their air packages. All the cruise lines charge for the transfers one way or another, either by charging a higher price for the flights or by showing a separate charge. Princess has opted to show a separate charge on your billing.
If you wish to stay at a hotel for a few days at either end of your cruise, Princess's "Cruse Plus" hotel packages include both transfers (pier-hotel and hotel-airport or vice versa). If you book the hotel on your own, the transfers are your responsibility -- but check with your hotel because many hotels do offer either complementary or very inexpensive shuttle services to or from the nearest commercical airport and, in some case, to or from the pier.