There is no difference in the food scenario. With your reasoning, the food should just cost more and the waiter paid more. Some guides own the business and can price it how they want and others work for a service and don't have that ability. (just like a waiter)
If you really understand the concept of gratuity, this isn't difficult.
There is a huge difference between a true guide and an on the water uber.... for the agreed upon price, you ride on the boat and have access to water/fish. Here is where the gratuity comes in- A good guide will hustle and help you read water & conditions, with tackle selection, casting, fishing theory, finding and catching better fish and in some case even more. You will usually take away knowledge that will help you find and catch in the future, in any water. The uber ride, plus a little more, is the agreed to price... the gratuity covers your appreciation for the rest.
Bottom line- If you appreciate their hard work, tip them well.... if you don't, they will likely find them already be booked on the dates you want to go back out. ?