Note that the ability to concentrate fire can be a huge advantage, especially when fighting a warship, where you're going to want to put as much firepower as possible on target.
The size restrictions aren't so serious-- to be blunt, you want more, smaller dropships when attacking cap ships because most large capships can pretty well kill any dropship, no matter its size with a very few volleys. More targets, even if they're individually smaller, is a good idea.
This true, but not the whole picture. The Castrum for example can do the same thing to the smaller warships, one on one. And it does take several of them a few volleys to destroy a single Castrum back. An aerodyne would struggle to come even close to that capability, where the Castrum is basically a small warship in it's own right.
I think you would have to get all the way past heavy cruisers (Agememnon, Sovetski Soyuz) to run completely out of warships that a Castrum doesn't have better armor than, and it matches or exceeds the fire power of several of the smaller warships by itself.
An aerodyne's structure weighs more, so they have to give up more to get to similar SI levels, however since max armor is based on the weight of the ship's SI, the aerodyne could have more armor than an otherwise identical spheroid, however with the size difference in how big they can go, 100,000 ton spheroids far outstrip what any aerodyne DropShip can manage by a long way.
Spheroid is what you use if you want your DropShips to go toe to toe with warships. Huge amounts of small aerodynes is what you would go with if you want to throw what amounts to disposable DropShips at your enemy. However, if you were going to go the route of disposable firepower, personally, I wouldn't use DropShips at all, I would use aerospace fighters, because they are vastly more effective at it. Ton for ton, you will kill warships faster with aerospace fighters than with small DropShips, and unlikely as it sounds, aerospace fighter pilots are more likely to survive than a DropShip crew. They are also easier to replace than whole crews.