I'm not convinced that moving the Pyramidion's hull armor to top deck would really increase the use of side guns. More so since the new buff to its stats encourages ramming.
Let's think about this:
Ramming under fire with an engineer, gunner on top deck:
What I see happening is the top engineer would work with both components and in dire circumstances, ignore the balloon to concentrate on repairing/rebuilding the hull armor. The gunner would only assist if hull needs to be rebuilt since the engineer is better equipped to repair. So the gunner and pilot deals damage to the enemy ship and breaks their armor... the engineer can't follow through with mortars. So great, meta isn't as op, but the engine engineer doesn't get any action unless the pilot turns right or the enemy dodges. Both of these cases are unlikely to happen. the first, turning to right so side guns can fire is silly. There are two perfectly operational guns on the front with two (as opposed to the one on the main deck) people potentially being able to fire. Even if they can't, the pilot can ram again as often as he'd like. The second case depends on the enemy ship actually dodging into your side arcs. Now ignoring the facts that the enemy ship can move in four directions and experienced pilots would avoid going into side arcs, the engine engineer would still not be able to put out constant fire. After missing, the pilot is going to turn the ship to retry ramming because we know from the first case that having up to two guns firing and being able to ram is better than always having one gun firing. That could mean phoenix claw gets used, then shortly afterwards, more moonshine. The engine engineer still has to fix the engines even if he is able to fire.
Ramming under fire with two engineers on top deck:
With two engineers on top, that means both engineers can focus on only one component and their guns. Also since there are two engineers so close to each other, that means only one fire extinguisher is needed, so both can bring buff hammers (For example, Balloon engie brings Wrench, Buff, Ext while Hull engie brings Mallet, Spanner, Buff). Because both engineers to keep an eye on their component as well as firing, they can't be relied on to consistently firing or ready to fire when hull is down, so I can see captains getting rid of the meta entirely with this crew formation. Instead, going for guns that work well together regardless of whether one or both are being fired at the same time. gatling-banshee, hades-artemis, carronade-flamethrower, as well as doubling up on the same weapon (Keep in mind it doesn't matter how well these combos can kill ships, only if it doesn't matter which gun is firing first.). Now, when ramming the enemy while under fire, both engineers can consistently fire their buffed weapons unless their respective component or gun is broken. After the attempted ram, we see that we have the same two cases shown above, except this time the top guns are buffed, and no component is neglected. So there's even less reason for the side guns to be used. Even if you give the engine engineer a buff hammer, chances are the engie is going to use it to buff the engines so the ship turns or rams faster so the bottom engineer still won't get to constantly fire his gun and is still the 'moonshine slave'.
So I can't see how moving the hull component to the top deck allows the side guns to be used more without pilots deliberately trying not to do as much damage as possible. And if the pilot doesn't want to ram but fire from the sides, why not go with a junker that can do both sides and have a higher hull armor, or a galleon that has nearly the same top speed and acceleration as a pyramidion, but with bigger guns? I understand that you want the engine engineer to fire with the top deck crew members, but I don't see all guns firing at the same ship. Could you give some examples of what you're thinking of with full shooting?
