You're correct that the structure may induce separation under some conditions. However, the effects are unlikely to be significant given the (publicly) available data on the concept. From the available images, the deck is quite small, with a seating capacity of only two.
Image from gizmag.com
Also, it is located at some distance in front of the vertical fin and appears shaped to reduce drag.
Image from technology.org
The company says that it has over come many design hurdles including
... structural modification, structural integrity of the canopy to withstand a bird strike and flight loads, condensation, noise levels, UV protection, aerodynamic drag, potential disruption to the vertical tail's performance, safety, ingress and egress requirements per the FAA requirements.
Though this should be taken with a grain of salt (it from the company after all), there is nothing insurmountable in the engineering sense. For example, the canopies of fighter jets are of similar size in smaller aircraft and they are operated without problems.
AWACS aircraft routinely carry huge antenna on top of their fuselages; they have no problem flying, albeit with reduced performance. For example, the following image shows the E-767, the AWACS version of Boeing 767 operated by the JASDF.
"E-767 Japan AWACS 112010" by Jerry Gunner - AWACS Boeing E-767 of Hiko Keikai KanseitaUploaded by Altair78. Licensed under CC BY 2.0 via Commons.
However, it is another matter if this is going to enter into service. My take would be that this is not going to happen in current time for a number of reasons including:
The cost quoted is pretty high and downtime, too long.
cutting up pressurized fuselage is not a good idea.
The concept is going to take up seats and increase weight for questionable benefits. What are you going to see up there? the same clouds that you are going to see from normal windows anyway.