..that winds up placing the bottom end in the Botanical Garden (Is it sufficiently shown on screen that the row of blue windows is in fact the Botanical Garden?) which again runs afoul of practicalities.
There are no sufficiently close-up close-ups of the windows in the original ST:TMP (where a photograph of trees inserted behind the transparent squares reputedly was used), and I don't think the DE makes a difference in this respect. In TOS, the garden didn't have large exterior windows, and indeed one wonders why such things would be necessary or even possible in an arboretum. Surely the extreme variance in starlight would be harmful to the plants?
One also wonders why an arboretum would glow blue from the inside. Plants normally have little use for blue light, and the users might wish for something more "natural", too - as seen in the TOS interior scenes.
In that respect, it makes perfect sense that there'd be a blue-glowing piece of high power machinery right behind those windows...
Perhaps the "windows" are no more vulnerable than the comparable blue-glowing things on the sides of the nacelles? Perhaps their function is the same: to allow an intense subspace field to radiate out, with some parasitic blue light emissions to accompany it. For all we know, those blue squares were a vital component of the new shields in TMP, and actually the toughest spot on the entire hull!