I was confused as well, so I called someone who does amazing finish work and this is what he told me.I don't understand why a natural finish isn't an option. It's surprising to me that it's not an option with most companies. It's not as if it's a more complicated finish to apply.
It's not more complicated to apply, but it's a lot harder to find a good body to apply it to.
The body takes a lot more time to sand and prep and imperfections and inclusions in the wood can't be hidden underneath a natural finish, so you need to be a lot more careful when selecting body woods.
You also usually only want to do a 2-piece body at the most, since it looks the best... solid color bodies are as many as 3 or more, simply because it's less expensive.