Hallo Jason and thank you for your log comment.
You are true about the price, if you should do this tour by yourself you spend less : boat to Bellagio with queue, boat to cadenabbia with new queue, then you can't go to Lugano, unless you come back by city bus to Como and take a new train, without nobody that explain what you see etc. etc.
This kind of tour, mine and of my competitors has this price because they are all inclusive package to see in one day these 2 beautiful town, easily from Como