Hard part of this question is that we never saw most of the TOS Enterprise's interior. So things like the big rec room (less windows). The big cargo bay could have been there in the TOS ship. Docking ports behind protective covers. Malnuvering thrusters, without the "look here I am" paint job. The "warp core" too, just never seen. The torpedo room could have been near identical, just moved to a new location.