From my experience the 10 square feet per chicken rule only applies to birds not allowed to free range. Since you stated they will be able to do so, I still say 8-12 birds max for full size and double that for bantams. Our current coop sounds pretty much identical to what you are describing with the exception that our nest boxes are in the henhouse with an external egg door so we don't have to go into the coop to collect eggs, but they are raised off the coop floor with is the full 4x6 feet. We've never had an issue with pecking (except during newbie initiations) or disease, and our coop is completely covered in clear plastic roofing material that lets in lots of light but keeps the inside of the coop dry which not only helps with disease control but odor too, as a wet coop is a stinky coop! The henhouse is raised two feet off the ground allowing for that extra 4x6 foot space to be used as part of the run and stays shaded most of the day.
And I think some people are confusing the 4 square feet per chicken rule to California State law, which says that chickens must have a TOTAL of at least 4 square feet per bird not a separate 4 plus 10. While I agree that the more space you can allow for your chickens the better, I don't understand the reasons for so much space given for the henhouse when the chickens will only use it to roost and lay eggs. Of course, if you can make the coop 4x8 and the run 8x12 that will be less cutting because of standard lumber sizes, so that might be another thing to keep in mind! If we were to do it all over, while completely happy with how ours turned out, we probably would've gone that route and saved ourselves the hassle of all the extra cutting. Then again, bigger coop equals bigger price tag.