We are very new to chickens and just finished building our coop a couple of weeks ago. I like having the nest boxes accessible from the outside just for ease of collecting eggs. It's simply easier to open doors and grab eggs then to navigate past food, water, roosts, etc to get to the nest boxes. Plus, it frees up more floor space. We will see how we like it in the long term, but I am in the coop every other day filling food and freshening water, so one less thing to go "in" for is nice. And the chickens free range/pasture all day so we see and interact with them plenty. I do agree that it is merely a preference thing though. I will post photos of our coop later.
Tracey