The new film muddles the matter further. The Enterprise has a second shuttlebay. It has at least 72 launch tubes in the secondary hull that are located on the sides of the ship. And it has a big white blocky thing that houses a "thing" that is the reactor. And it has a multi-deck circular room with "bridges" that connect corridor segments.
Are there actually 72 launch tubes?
I actually got the distinct impression that Admiral Marcus had Enterprise retrofitted with the new launch tubes specifically for the Kronos mission. I mean, it wasn't a minor thing that had Scotty so pissed off that he would rather resign than authorize them being brought on board; it was literally a totally unknown weapon system that had never been used before whose exact specs nobody understood.
It would be the equivalent of an aircraft carrier having a half dozen ICBM launchers bolted to the flight deck. The Air Boss is probably gonna have a problem with this.