The boxer engine is short and low but wide.
I would be more concerned if the conversion raised the CoG higher than the boxer.
The motor is similarly short, much narrower, and just as low. Of course motors often have a controller and other components sitting on top of them, while boxer engines have intake and other accessories sitting on top of them.
In this conversion, the motor shaft takes the place of the engine shaft, so the motor and engine are at the same height. There's no problem with this, but it's a missed opportunity: the motor doesn't have a sump, so it could sit lower and maintain ground clearance if it were not constrained by the stock transmission position and whatever structure runs under it.
In a normal Subaru, the engine is very high, to place the transmission input shaft over the differential. With the engine in front of the axle there's no way to put a steering rack up there, so it runs under the transmission. The BRZ/86 adaptation keep the rack position (for the same reason, even with the engine shifted back somewhat) and that forces the transmission to stay high and keeps the engine and transmission from going further back. The starter motor also prevents the engine from being further back, as it would run into the firewall. After the conversion due to the differences between the boxer engine and and electric motor, the vehicle could have a desirable front-steer configuration and the motor and transmission substantially further back... but it's stuck with the compromises caused by the boxer. A conversion of another Subaru, again using the original transmission, would need to keep the transmission in the same place to line up with the front axle, so these placement issues are unique to the BRZ/86.
The big centre of mass (CofG) issue is usually the battery. In this case, most of the modules are quite low (in the trunk, in the fuel tank space, and flanking the motor), although some are stacked higher in the engine compartment. That's a lot better than many conversions. The part which is unfortunate about the mass is that most of the battery mass is too close to the ends, rather than within the wheelbase. That's the result of the small car not having any other space, and the configuration of the motor taking the prime underhood space. At least it's much better than stacks of modules (or lead-acid batteries!) stacked over the motor and all the way to the nose, as has been done with other conversions of other vehicles.