I actually don't think submerged factories are tings that belong in a mobile (or temporal) base (which is really what the base you build yourself is). Stationary bases could have submerged factories or maybe even a huge underground construction (which you'd have to infiltrate in a mission or something; so you'd have an inside mission like in Red Alert), so I think it makes most sense if the underground constructions would be rare for Nod.
I imagine that the Scrin (during the assault on Earth only though) would have a couple huge mothership near earth, which would teleport units down to whatever platform has been built to receive those units (so let's say the Scrin can only teleport things between 2 of their structures). On the Scrin planet the Scrin should have the same factories that are present
on those motherships, so on the Scrin planet you'd see the Scrin constructing units in the traditional way.
I agree that having underground (or at least partially hidden) buildings makes the most sense for the Scrin rebels, so giving them a partially submerged war factory sounds like a good idea