How does a vertically higher center of gravity affect handling?
As long as flight is coordinated, the vertical position of the center of gravity (cg) is of minor importance. It will show in issues like thrust changes, when acceleration will cause higher trim changes because of the increased lever arm between the inertial forces and the thrust forces.

This will only change when flight is no longer coordinated and the aircraft sideslips. Now the big cargo volume is more important than the cg location because it will contribute a considerable side force. Also, it will need additional means of lateral stabilisation because the big fairing will destabilise the aircraft in yaw. Still, the lever arm between the cg and the lift force vector will be much, much smaller than the lever arm of the ailerons, and a little aileron deflection will be enough to stabilise the aircraft.

Maneuvering will look funny to crews used to fly the unmodified version of the same airplane, because now a roll manoeuver will induce a lateral motion at the location of the cockpit which was not there before. Same goes for eigenmodes like the Dutch roll which will be more noticeable for the crew because their cockpit sways laterally.

"Flipping over" needs deliberate commands from the pilot; this is no different in aircraft with unusual vertical cg positions. The most extreme is probably the VM-T "Atlant" version of the Russian M-4 Molot bomber.



M-4 Molot version VM-T Atlant with Buran booster tank (picture source)