I wasn't saying that in-game this ship would only be fitted with 12 guns -- just that that's probably closer to the historic reality.

Note that I wasn't completely sure about the forward ports, too.
We can probably fit guns behind them even if there isn't room -- no one's going to be able to see how crowded things are there. But you will want to double check the clearance on the 2nd pair of ports and ensure your guns don't recoil into anything, as those guns
would be visible.
Similarly, for the captain's cabin, we can and probably will ignore the fact that even though guns might fit there, it would be rather challenging to get them in place in a real ship

If there's a hatch on that deck, that makes the fiction of a gunhappy captain sharing his berth with a 6-pounder all the more believable.
The two middle ports right by the main deck would be problematic, though. The cabin roof would very obviously interfere with the operation of guns there. And more 16-20 gun ships are still useful for the game
