Admittedly I'm putting a lot of emphasis on a single example, so you may be right. But on the other hand if you look closely at the pixel art (which I have, arguably inadvisably so) the RFL seems to load vertically and a magazine above or below the firing chamber would most effectively facilitate that.
Plus, a fully linear one-deck arrangement wouldn't really solve the problem - the only space for a single centreline launcher would still be on the upper hull with the same issues (cutting into crew spaces, needing to run an antimatter line up that far), and tandem launchers along the rim would still be way too expensive.
I think you're overthinking this. The place on Deck 4 where you already drew a two-deck launcher on your diagram would work fine, even assuming it needs two decks as a design requirement, which it probably doesn't.
Like either way, there's plenty of space:
The two-deck setup does have the advantage that it essentially cuts off the curve of the saucer and leaves a nice rectangular two-deck space which is easier to fit modules in, so I expect @Sayle might go for that? But either way, we've got plenty of space for a single frontal launcher.