A good solution for both could be to tie the armour placement explicitly to the location of components you could place freely, and show the outline of the armour and vital areas when placing those components. For instance, machinery is under the funnels, and the belt extends between the forward and aft main turrets, or the machinery spaces in the case of an all-forward design. Then the citadel type would explicitly determine the performance of the armour versus varying types/angles of hits, and have nothing to do with the placement of said armour.
The opaqueness of the present armour placement scheme is the main problem. I would really like to know where the armour is going and how much my layout choices affect its placement, weight, cost, and impact on ship stability, but right now we can see nothing. It's frustrating to have all these numbers under the hood.
Gunnery... is pretty frustrating at times, but I'm starting to wonder if it's even worth talking about. I was browsing threads back from the middle of last year in which some pretty knowledgeable people (including yourself, iirc) were pointing out the problems with the system. I've only been playing a couple months and I've been submitting bug reports and suggestions, not knowing they'd already been raised ages ago.
So to bring this back to a genuine question for the devs: we're in alpha, and you still have the time, and access to people here who seriously know what they're talking about. Do you have any plans to work on the gunnery model based on community analysis and testing - or are we just going to see a series of tangential hotfixes addressing individual issues, that create balance problems of their own?