In general, I agree that it is typically cheaper and "fuller featured" to book direct, which is usually what I do. ...but at least in the limited cases I've looked at so far on my Princess cruise the text in the write up is almost verbatim what I'm seeing on the web from independents, and here is a sampling of prices.
WhitePass Rail: Direct<$82> Princess<$89>
MistyFjords: Direct<179> Princess<189>
Mendenhall: Direct<169 for 55 minutes> Princess<189 for 75min>
There's always the case of possibly comparing apples to oranges, and the cruise ships can always bump their "tour times" by including transport to heli-pads, rail stations, etc. but this price uplift is the smallest I've encountered so far (8-9% uplift). However, at least they do deliver you to the operator, if you book yourself, getting to the operator is your responsibility.
I don't like paying the uplift at all, but I've also had friends that were burnt by independents when their ship had to change itineraries without notifying the passengers ahead of time (hurricanes can cause a ship to run the itinerary in the reverse direction, port problems etc. Read the fine print on that book contract!) so there was money/deposits that were lost to the independents ranging from 10% to 100%, money that was lost when the weather was inclimate, poor service from operators, etc. Granted these are rare, but it does happen. So, you can think of the uplift as a type of insurance. I have had three occasions where I was glad I booked through the ship (usually when I can't find an independent): 1) I was very displeased with the operator (tour operator equipment problem - RCCL refunded 80% of the tour), 2)severe weather yet the tour was still "on" (I was able to cancel at the time the tour was to depart for 100% refund),3) changed my mind after reports from people on the previous excursion (100% refund). I also have a friend of a friend that was "left behind" on an island because his "private tour" got him back too late due to equipment problems and he had to pay the cost of catching up with the ship.
Sooo there are pros and cons both ways...
So, there are multiple ways to look at it, and if you're the cautious type that usually buys trip insurance for example, then maybe booking through the cruise is for you (easier, faster, safer, little to a lot more expensive). However, if you like to maximize every minute and dollar, booking direct is the way to go. For me, I'll be booking direct (but then I never buy trip insurance :^) if I can cancel at the last minute, but some independents I've looked at are charging a 10% cancellation fee so I'll steer clear of them. Also, if booking direct, do it in advance. You don't want to get to your destination and have to hunt for an operator or find they are sold out (e.g. WhitePass Rail).