Well, it depends how you want to look at it. Since Mr. Jefferies suggested that this Enterprise was almost the same as the original, with changes to "struts and power pods only," we might assume that what we're looking at his his intentional effort to revise some aspects of the original design. Now, we know there were a few other cosmetic changes, such as to the bridge module with the addition of another turbolift, and the apparent addition of visible airlocks, and it's certainly possible (and perhaps likely) that the vertical core was also a change or addition. Still, there are some distinct changes to deck spacing here that seem to normalize and make more regular certain features shown in the famous Writer's Guide/TMoST cutaway. If the vertical shafts are indeed power shafts rather than turbolifts, then I could see one engine room directly ahead of the impulse engines, with the vertical shaft being a power conduit leading down through the neck, then horizontally "jumping" aft to another vertical shaft, which the Phase II engine room would be oriented around, and probably the TMP-style horizontal shaft going back to the struts. Since both of these features were present in the TOS cutaway, we should probably assume that this was then unchanged from TOS to Phase II.