Sure. But as I said earlier, as tempting as it is to look at those slots in the ship designers as real, physical, turrets -- they're not. (Otherwise many famous ships would be unbuildable. The Bismark had four turrets, not two; the Nelson had three turrets in the front, not two and one; both are represented in the designer wtih two heavy battery slots.) The slots just placeholders for a range of number of guns of varying sizes, and recreating some historical ship doesn't call for N main battery slots just because the ship had N turrets. So you can't really tell from the clicks you make in the ship designer how radical the changes to some ship (likely a fictional one from a player's imagination) would have had to have been.Though that was replacing existing turrets with new turrets and they had to reduce barrel numbers to allow for that.
Maybe the historical Gneisenau upgrade should be represented just an upgrade of battery types in the existing slots. Maybe it calls for adding the third slot because the guns are so much bigger. That's a question more detailed than the abstraction in the designer.
But my main point was just a response to the suggestion that main gun refits should simply be outright prohibited by the ship designer code. There's a big difference between "worth it only in rare cases, maybe abandoned as resource demands change" and "not physically possible because the laws of the universe prohibit it and no naval architect would even consider that kind of change no matter what their time and resource budget". I think HoI4 is actually getting the model right if those major refits are possible, yet only rarely used because most players find redoing major chunks of capital ships too expensive and/or time-consuming to be worthwhile in the press of active war demands.