That's a real good question. I work in tourism and I'm thinking about this real problem for tourists coming to Egypt. I will tell you the best for you and the other side as I know all the details from both sides, and i wish you can have sometime to help me with your opinion to find a solution to this problem to make easy for tourists.
The best way to have good prices and services, you book the tour before you arrive to Egypt and you know all the details you need. Payment to be made cash when you arrive.
I know Expedia or many other non Egyptian companies may not do that unless you pay. You better do it through an Egyptian company to pay the real price of the tour. Any transaction made by credit is charged by the credit company and banks. It takes about 48 hours to be added to the account of the one who offer the service. The bank transfer takes longer time, but it's safer for bigger amounts (it's also charged high charges more than what you pay to make the transfer).
The most important for tours in case it's not a group, is to book all details and confirm with your agent in Egypt. In case you can pay in advance for tours, that would be good as travel agencies pay to book cars or buses if they don't own. Also tour guides are freelancers in most cases that means they can be busy if not booked in advance. Hotels receive their payments in advance if it's not a charter trip or regular with the travel agent.
Also you should know that tours cost can be very low in case of groups, because we have fixed costs like bus, tour guides and other costs which can be the same for 1 tourist or a group. If you are going alone not sharing in a bus with a group, the prices you mentioned is low compared to costs that I know.
Good luck and you can send me if you need any help