I'm really not sure how you could do the tiered weapon mechanic in the game. There... really isn't a way I can think of to do it without fundamentally changing the game. The captain brings the weapons aboard the ships, correct? That means that the captain, who would most likely be a higher level, would have control over what was brought aboard and what the gunner would have to use, as it is now. Tiering up the weapons... how? Make it so that the gunner simply can't use the weapon until he reaches a high enough level? Make the weapon change when the gunner uses it? I just don't see how to implement it properly in that case. The captain is the one in charge of what weapons he brings, meaning that the captain would need to pay attention to the skill level of his crew and change the loadout from there. I don't mean to be rude, but would you mind telling me how you want to tier the weapons? How to implement it and everything?
I like the locking down mechanic, but it might just be easier to simply keep it locked. More teamwork involved between captain and gunner, but I like the argument of letting you lock it down before firing. That'd give the gunner enough control over his own weapon, while still requiring skill to use properly. Perhaps a moment or two for the weapon to actually lock down?
For the buff over the lockdown, I would say firing speed. The wepon is locked into position, right? Meaning that it is stable and not needing a pause so as to not stress the motors and turntables that the weapon would be built on. Lock the weapon down, and it can fire a little faster, but it cannot change arc. The recoil mechanic would be the same, meaning that it would be marginally frustrating as the ship keeps getting kicked back a bit, but you would be able to send more rounds out a little bit faster before the ship needs to be made stable again, and the weapon needs to be aimed again. That would make it a mid-high level skill requirement, where lower level players can just use the primary fire at a slower rate, but with the same power, while a higher level player can lock down the weapon and attempt to barrage an area while the captain, of similar skill, tries to manage the recoil as best he can.
Problem with that would be Impact Bumpers. A Captain could probably just throw on the bumpers and hold position from cover, using the locked down Atlas to simply pour rounds into an area, adjusting the ship on the reloads so as to keep the rounds pointed at the enemy. I do think that that would make the ship a target for a faster, more maneuverable ship that would be difficult to hit by the Atlas, which might balance that a little. It really would be artillery, in that regard, needing to be set up behind a wall of quasi-infantry like Pyras or Junkers so that it could effectively shell an area. Not the most obvious effective use of firepower, since everyone wants to go for the hits, but it's the nonobvious power of the weapon, morale. No one wants to go into an area that has Atlas rounds pouring out of it, just like no one wants to be on a Galleon's broadside when they're running double Hwatcha. I've had heartattack moments on Paritan when I start to cross one of the streets and walk directly into those lions, same could be said for the Atlas.