I lost the shortened version of my CruiseTour journal (the original is 110 pages) which I had intended to post since, like you, when I was planning I found very little in the way of CruiseTour reviews. If you have more specific questions, send me a note at the email above and I will do my best to answer. Keep in mind that my responses are based on a 2001 experience, and some things may have changed post 9/11.
Whether meals are included, depends on the kind of CruiseTour you booked. We did an escorted tour with Princess last year from Anchorage to Prudhoe Bay and back, with stops at Denali and Fairbanks en route. With the exception of one or two lunches, all meals were included, including dinner at a restaurant of our choice the night we arrived back in Anchorage. (The same itinerary, unescorted, did not have meals included, but facilities were available to purchase your own meals -- expensive from what I heard.) The itinerary in the Princess brochure should state specifically whether meals are included and which ones.
We went on the CruiseTour for one primary purpose, to go up the Dalton Hwy and reach the Arctic Ocean and we did not want to travel the Dalton on our own. Everything else along the way was "gravy" for us. We knew in advance that by doing a CruiseTour, we would not necessarily be able to spend as much time as we wanted in Denali and Fairbanks, but were OK with this since we knew this would be one of many trips to Alaska for us.
The pace was not as hectic as I had anticipated. We had time to ourselves in Denali and Fairbanks, and most of the two days on the bus going up the Dalton was just sitting around and looking for wildlife while a competent driver took care of the navigation - frequent stops were made whenever animals were sighted. We never felt like we were being herded from one point to another. Daily departures were around 8p or so - not a problem for us because we are early to rise and get going even when we are on our own. We did have a good group, and by that I mean that everyone was always on time - we never had to wait around for stragglers, which could have been a real bother.
Luggage-wise, we followed Princess's recommendations. If I read your post correctly, you disembark in Seward/Anchorage and then fly to Fairbanks to start your land tour. I would imagine that they will store any luggage you do not want to take with you on the land portion until your return to Anchorage. With limited cargo space they will not want to unnecessarily transport all the excess luggage around. Our cruise luggage stayed in Anchorage and was sent directly to the ship on day of embarkation along with the rest of our luggage which accompanied us through the land portion. On the Anchorage-Denali portion of our trip, our luggage was trucked to Fairbanks and we had an overnight case with us on the train for our one-night Denali stay (very limited storage, so be very selective with what you take on the train). In Fairbanks, we received all of our luggage (delivered to our room), and packed clean clothes in our carry-ons for the mid-way stop on the Dalton. All of our luggage went with us on the bus to Prudhoe Bay, but the only items accessible were the carry-ons which were loaded in a separate compartment under the bus. At Prudhoe Bay, we again received all of our luggage (delivered to our room), and the following day everything was checked in by Alaska Air (right at the hotel) and loaded into containers that were then loaded into the cargo compartment of the flight we took back to Anchorage. Whenever we had all of our luggage, all we had to do at the appointed time was to set it out in front of the door and staff collected it and loaded it so we never dealt with anything but our carry-ons.
Seats on the train are supposed to be assigned. Our group had the entire front section of the last car on the Midnight Sun Express, and our escort opted to let us pick and choose for ourselves. (If you have a choice, southbound, try to get a seat on the right side of the train between Denali and Anchorage (or the bus, if they are bussing you back from Denali to Anchorage - probably more important if you are on a bus - Mt McK will be on that side.)
Since we opted for an Escorted CruiseTour, some of our shore excursions were included in the total price as well. Those that were included were things we would likely have chosen for ourselves anyway, so it worked out well for us. There were also group get-togethers on the ship, with our escort buying us a round or two of drinks. Free group photos at Margerie Glacier were included as well.