What you should always keep in mind is the fact that if a developer does not add a visual setting to his application (or to the system settings), he has a reason for that. elementary OS tries to provide a good out-of-box experience with sane defaults. More settings visualized in your application means there is more stuff that can act unexpected or break the overall user experience provided.
That being said, most apps in elementary OS contain those "advanced settings" available only via dconf-editor because sometimes, default just doesn't suit you. But it's some kind of "last resort": If it's not available via setting panels, it's not well supported - It might work, but it could result in a suboptimal user experience. That's why it's "hidden" away - The developer does not think it's a great idea to use it. Sometimes, dconf keys are not "user settings" at all; They're used by applications to store user-specific values as well.
To make it short, dconf should only be used if absolutely needed. Try to change things via setting panels or the system settings before and always be careful if you're using dconf - If you don't understand what you're changing exactly, it might be not the best idea. Try to understand what you are about to do before you do it.