But really that is a bug or just a bad implementation. The fact that multiple smaller modules can provide the same advantages as one larger module but with much lower disadvantages has always felt like a nonsense to me and I would expect that to be adjusted if what I have asked for was built because it is wrong now and would just be exaggerated then.
Alternatively it could be an attempt to balance things out a bit. Looking at ship sizes and internals, i would even say that FD went softly there. They could've pushed the values even more in favour of smaller internals and the game would've profited from it.
So really, it's more than reasonable that things are like this. Nothing bad about it.