Yes, some will ONLY book ship sponsored tours. I get that.
But, if you book on your own with plans to be back 2 hours before "all aboard", that leaves you plenty of time to deal with traffic. And as said, often it is the same traffic as the ship tours.
We prefer on our own for many reasons. Smaller groups - 2-12 is the norm for us. Less waiting for others. More flexibility, especially if nobody else is with you. And the cost is the same or less.