That would just go backwards in updating when it comes to progress. The pilot can help easier even with the gunner on this current set up. For your second suggestion, it would make the spire more tanky but by design inside of the ship wouldnt make for a fun gameplay or splitt the players how the players should be.
I would move the hull to where the baloon was (Next to the stairs on the upper deck). That way the spire will be tanky in the sense if focused.
But the reason for putting it in the lower ramp is to delay that sudden repair by just a bit. When the baloon was upstairs, it was repaired/rebuilt fairly quick, perhaps quicker than the junkers baloon.
But the focus took its time because the baloon is tough to rebuild/repair. The hull is very easy, and so the delay is balance to the sudden rebuild making it Tanky like a goldfish or squid.
In some aspects kinda enforces 3 engie 1 gunner combo.
There is actualy no problems with the set up we have now, it is actualy more beneficial if the gunner and the pilot take the extra step to run up or down a ramp to repair the hull.
But no really... the spires aspect is very hard to see, it being not so glass cannon like will end up force ships to try and counter it directly.
The only ship that is directly countered with extreme specific choices is the junker. And that is not because of its stats, but rather its Form. The junkers baloon is huge but the hull really small.
So people result to punching the baloon of the junker instead. But it has strengths against it like the baloon being easily accesible by the pilot and an engineer so the baloon can always and will always be repaired quicker than most ships. (Excluding the squid, the squids baloon is pretty quick).
The thing im suggesting for the spire is to Use its form. It is slender, and like i said. People do miss it if it goes side by side. Problem is, it isnt that much and is equal to other ships.
The junker has a hard armor to hit along with tough armor. The Mobula is horisontal and has a baloon underneath, it goes up and down fast. The spire may as well go Horizontaly and turn fast because it is a vertical shape. It is a very simple concept.