Weight distribution as mentioned above. But also, the boxer has a much lower height. This lets the car have a lower hood while at the same time meeting pedestrian impact standards which state there has to be X distance (7cm I think) between the hood and the top of the engine.
I like the boxer design, personally. Plugs are difficult, but no more than (and possibly easier than) doing plugs on an LS1 f-body. But they have a low CG, are naturally balanced, and can be reasonably torquey in N/A trim.
People just have to remember that the FT isn't supposed to run with the Mustangs and Corvettes. It's not a replacement for the Supra. The point of this car is to make a fun, nimble, relatively low-cost RWD sportscar. 0-60 will likely be in the 6s, and 1/4mi will be 14s at best. Think more Miata style performance.
The FT will occupy a very different niche. I doubt serious buyers will cross-shop a 180hp $20K RWD coupe with a 300hp $35K AWD sedan.
That said, car manufacturers have made enough inconceivable decisions in the past that I put nothing past them.