Henry Huddelston Rogers donated his collection of model ships to the Naval Academy when he passed away in the 1930's I believe. Look him up, he's an interesting man.
I see you noticed that the main rail would overhang on both sides but on the model it is flush with the interior planking. That's the fun of this particular build. You can choose to follow the Rogers model in the Naval Academy when you want to or you could make your build a little more accurate.
The Rogers Model for example does not have a waterway however the kit properly shows one. The mast top is simplified in the kit and matches the Rogers model as well. It's up to you to detail or not.
Takes the pressure off of everything having to be exact. A lower level of detail in a consistent manner would not detract from the final result. Not saying that anything goes, that would be bologna, but you can relax a little and if you miss something you will still have a beautiful model in the end.
If you're looking to go bat guano crazy I posted a list of good resources for people to use, search Fair American 1780 general information.
Bruce