KeithVXlvr--- First, I totally agree with your analogy of classic Mustang's with/without a sunroof. However, classic Mustang's never had finicky OEM window problems from the factory like the VX. Second; it is customary to modify the VX to various degrees, as opposed to a classic Mustang. Third, if I saw two(2) identical VX's for sale parked side-by-side (same aprroximate mileage, same color, etc), and the only difference was one VX had a professionally installed electric moonroof-- I'd buy the VX with the moonroof, without hesitation.
I have an electric moonroof in my VX (installed by P.O.), and I use it every time I drive the VX "in lieu" of rolling down my side windows, as the side windows can't be trusted without fear of getting stuck in the down position or coming out-of-track. Having experienced the electric moonroof in the VX, I can't ever imagine ever owning a VX without one in it-- yes, it is that sweet.
My electric moonroof was professionally installed and looks/operates OEM factory and is totally leakproof in torenchial Washington State downpours.
In the case of the VX, I would honestly say that a professionally installed electric moonroof will actually "increase" the value of the VX. Especially due to the VX's inherent side window issues and the fact that it is accepted protocal to modify the VX to varying degrees of modification (lifted, super-charged, K.E. skid-plates, etc).
On the other hand, a cheapo "pop-top" sunroof in a VX gives free gratis for the VX owner to get his @ss-kicked, because he took the cheesy way out. Either get the professionally installed electric moonroof, or don't frickin' do the modification. Go big, or go home.
The biggest hurdle is shelling out the $1,200 (+/-) for the professional electric moonroof installation. However; once you experience having it in your VX, you'll wonder how the hell you ever lived without it.