The other thing to bear in mind when looking at these is that (for practical model-building reasons, mind you) these "skylights" correspond with the rim windows. (The practical reason is that they were all lit by a single light source... three for the saucer (with one just painted on and not really lit) plus a single forward-facing one and a top and bottom one.
So, in "in-universe" terms, these "skylights" are effectively colocated with the rim windows.
Now, in my opinion, the circular "portholes" are for sensors (they provide a pretty complete coverage for the entire ship, including upwards and downwards coverage). Inside of each of those little circular windows is some piece of sensor tech, observing through the porthole but accessible (and maintainable) from within the ship, in a shirt-sleeves environment. But the rectangular windows are "viewing ports."
So, we know that there are "personal observation windows" or viewing ports in the exact same areas as the "skylights" are found. Despite the "production shortcut" which led to that being the case (if the ship had been designed, from the beginning, to be illuminated, I wonder if it would have had the same set of windows?), it's still what we've got.
It just seems a bit odd to have a "personal relaxation and reflection" window set inside of one of the working spaces of the ship, filled with heavy-duty mechanical and electrical gear. (And yes, mechanical... most sensor devices we have today have a mechanical element to them, and I see no reason to conclude that this would change so that everything was "magic" in the future.)
But Alex has every right to prefer having those be a specialized "very large array" concept, and to build up his model that way if he so desires. In MY case, I'll be building actual setpieces made up to match "engineering redressed as an auditorium" and "engineering dressed up as a gymnasium" (and two other configurations I'll be making up largely from scratch, but which will likely also be "engineering dressed up as something" setups) underneath those windows.
If nobody else on the planet ever agrees with me... that's just fine. I know I'm right, so there!