So... she's not Maru-yu...?

She is Maru-Yu. If I'm not mistaken, she had little sister before he got transfer into the base. I think this one is her sister from many sisters.

the "Maru-yu" we know ingame and in works is actually a collective body of the Type 3 Submergence Transport Vehicle.

So basically there are many Maru-yu, each one is the same, while being different.