When it comes to fees, there are various cases depending on guides and guests.
It varies what expenses guests and guides pay in advance and on the trip day.
For example, it may be a cost of a facility that you can not enter without making advance reservations such as the Ghibli Museum, or an activity you need to make advance reservations and pay first such as ceramics classes.
Basically, guests pay these expenses in advance when guides send offers.
However, it completely depends on what guides and guests decide.
All you need is to consult about fees with guides.