The only reason to join a tour is if you want to pack in as much as possible in a day. Otherwise, the buses/subway in Kyoto are fine.

As for Tsukiji tour, 30,000yen can do a lot of other things. You can walk around the market on your own.

I have no idea about the specific tour you mentioned but in general, people like a tour because the guide has very good social skills, but you have no idea if the information provided is accurate, or merely to entertain the guests with tales.