...any idea if the decks will be the same height as the 23rd century cruisers or a little thicker here and there for bulkier machinary?
I'm envisioning about nine or ten decks in total with perhaps two decks running through the narrowest part of the ship in the middle, and once you cross over into the aft section there are two decks above you. I don't see all the decks being exactly the same height.
The bridge isn't meant to be at the topmost dome---thats actually meant to be an extensive space sensor array with the bridge the bulge underneath it. Engineering is just above the nacelle support and there's meant to be heavy radiation shielding in that support pylon. Yeah, you can go down through the pylon and eventually into the nacelle itself, but only in an emergency with proper equipment or (preferably) when the warp engine is turned off.
This variant of the design is the science reconnaissance version so it would have minimal armament, but it does sport extensive sensor arrays all around the ship. Additional laser emitters and missile launchers could be added to a modified variant of this design. In that event the two variants might look quite similar from a distance. Eventually Starfleet (which doesn't exist yet as my impression is Starfleet comes into being in the early 23rd century) would learn that you could have a ship with both extensive sensor arrays and respectable armament.
Besides a flexible spaceframe that allows variants to be constructed with relative ease the main strengths of the clipper are speed and maneuverability---so when fully armed it makes for a decent combat vessel.