As a former user of these services from one of these stations you are sort of right, people do generally aim to take the Cobham service to Waterloo as it is faster.In a similar way, I would be surprised if anyone between Guildford and Effingham Jct travelling to Waterloo would choose to use the Waterloo to Guildford via Epsom service all the way since the services via Cobham are much faster.
However, the combined service in the direction of Waterloo is 4tph and this is nearly turn-up-and-go, so people do tend to turn up at the station without having a specific train in mind.
If you are going to Waterloo and the first train is an Epsom train it usually makes sense to get on it as waiting 10-15 minutes for a Cobham train isn't generally worth it (there may be a couple of minutes advantage for doing so sometimes iirc). This is especially true in winter as sitting on the train is usually preferable to waiting on the platform if it is cold.