Ah, so you want an animated weapon that can render under the ship sprite and do some fancy animations. Like, say, a giant crablike character with the "claws" able to open and shut while their cannons animate, etc., which would be pretty awesome.
That goes into the same category as my turrets-on-turrets idea and underslung weapons in general; it's a pretty un-trivial change to rendering order; underslung weapons would have to get queued first, then ships, then regular turret bases, turrets, glows and so forth.
Technically, I don't see any major issues making it happen, other than it being a lot of work, but I don't know anything about how the engine's handling that kind of queue.
There are issues of pop-in as well, if ships started having huge, elaborately-animated built-ins; probably that can be solved by rendering any ship that passes a distance check for 1.5 view distance from the center - radius and then just requiring modders to use bigger radii if they want to avoid issues. I presume the engine's doing something like that already, so it's probably not a big deal to add that part, or even having a view radius variable per ship.