The first I think about it is that pop-up turrets are mostly to hide your weaponry when you're in a starport or similar situation.
In space when lurking for an ambush, if they come to a visual range where they will see it, it's too late for them to flee without combat. I guess the sensors are not enough detailed at large distances to distinguish the turrets, less so if you try to disguise them as you suggest.
I guess we forget all too often that ships in combat don't use to see each other, working only on sensors' readings, far away from visual range...
Unless it is a meson bay, that can fire through matter (and so you wouldn't even need to open the cargo doors) it would limit your fire angle, probably too much.
WOuldn't be easier to fill your cargo hold with fighters and (if needed) quarter modules for their crews?
Fighters seem useful, but launch and recovery takes time.
Why that configuration of ship? well, they are available, and the company, operating across the Imperiums boaders has reletively easy access to them.
Yeh, it is mostly to hide the offensive capability of the ship in a starport that I am thinking of. The Company will use this ship to move teams about, and act as support in case the target does a runner and hits space (pending clearance from the local law etc).
IMTU outside the imperium, just about everybody who can build star ships, builds Beowulf’s, and there are many variants, including combat versions. These are built in small early-mid stella states that want force projection on the cheap and can re-use commercial shipping yards. The idea has evolved and has been refined over centuries, starting with 2 turrets, then someone put in a bigger powerplant, then someon hot-rodded their engine, then someone added armour etc (you get the picture?) The ships either have a 2nd turret or a fixed forward triple missile turret (old Solomani style) in the ventral position, upped armour, upped power plants and computers, M3 or M4 drives, all the best tech level 9/10/11 can offer

. They have been given the nickname Hrunting types by the Imperium (after the sword Beowulf uses in the poem). Go a few parsecs outside the Imperium and you start to run into these.
Alone one is a trouble and a nasty suprise but usually can be handled, but they are usually never alone (they have a reputation of being pack hunters). To the point that the Imperial Navy's equivalent of a Kobayashi Maru test is to have cadets man a simulated 400 ton PT cruiser going in against 2 Boewulf Pirates attacking a freighter (and when they are in range, the pirates then power up to M4 and let loose 3 missiles a turn at them, the once overconfident cadets now find themselves in an almost fair fight). The Hrunting types are a controlled design within the imperium (you need a license to have one, you need a reason for that license, that reason is that you are a state government that needs jump capable police/customs ships, a corporation that needs asset protection in outlying areas etc).
So this ship is being based on one of those (asset recovery of an imperium based bank, that property might be outside the Imperium) that a company acting across the Imperium’s boarders happens to own at least one.
Why do these discussions always end up with meson guns?