Okay, so… I want to open with the observation that all the ships that have been attacked by the mysterious ship have been CGI.
Lower Decks tends to default to 2D unless the ship either will get a lot of screen time (California Class, Shuttles), offer fan service (Titan, Voyager, DS9, Sovereign Class), or get into combat (Bird of Prey, Clump Ship, Sh'Val, Texas Class, Green vessel).
Basically, Titmouse gets their money's worth from CGI models, and will use 2D where otherwise practical.
This season, as far as I can tell, all the attacked vessels have been CGI. Their screen time has all been extremely short. With the exception of the Bird of Prey (from 3 ships) all the attacked ships have been new to the series.
That said, their on screen appearances could've easily been substituted with 2D illustrations. Most of the ships barely move, which is perfect for 2D, but they opted instead for more expensive CGI.
Whatever McMahon has planned for these ships. it isn't going to be small.
With that stated. When the mysterious ship reorients itself to attack position, I can't help but feel like it looks kinda like a face. But humans are hard coded to see faces in things, so I didn't think much of it.
Then I saw the Bynar ship.
The 'nacelles' on the ship connect to a hub in the back… and it looks to me like hinges. Like the nacelles could arbitrarily reorient themselves like a pair of thighs attached to a hip.
Face. Hips. Legs.
The mysterious ship can't be stealing all these vessels for salvage. We've already seen that done with the Pakleds. The ship also can't be interested in these ships for their intended purposes, since there's nothing of substance that connects them all—beyond all having disgruntled lower deckers.
I don't know why they would do this, but I can't shake the feeling the mysterious ship is attempting to build something akin to Voltron or the Megazord. A giant bipedal mech made of a bunch of other ships.
Maybe the vertical Warbird is the torso. Maybe the Bird of Prey and the Orion ship are shoulder pads or feet. I don't know.
But I figured I'd bounce this idea off you guys and see if you could refute or add to this.
I have nothing to add here other than that I'm impressed with both your in-universe rationale and TV production rationale. This is solid Daystrom work and I hope we get to see the Trek Voltron. Even if it's not a literal anthropomorphic robot-ship, I think you're onto something.