You are not looking at it too deeply. Yes, it does effect the outcome. But what you don't realize is that the runes do in fact overlap much of what they are. Isa is in both and so is kenaz! Ice and Fire are the elements of creation, the birth of a journey, the hearth of the world tree. The runes seen individually will trick you more so than not. When seeing how they flow into one another, as everything in life flows into itself, you will learn the mystery, the secret--what Odin sacrificed himself for--understanding of the inner workings of the fabric that is our world.
When you create bind runes you are taking that focused essence and wrapping it up together for a specific purpose. The runes themselves will do as they desire if you do not give them that specific purpose. I find that in order to direct bindrunes correctly, you must include a goal, a compliment, and a guide. The goal is your main purpose, the compliment helps it along by making the purpose more precise, and the guide keeps it from swaying from your original goal. For instance if you use thurisaz, it could be very chaotic and destructive, much laying down bullets on a hot platform, but if you pair it with ansuz or algiz, it would keep it in line, direct it like the barrel of a gun.