I would have to confirm but in conventional aircraft design the engines are usually in front of and below the main wing. Firstly this would allow a maximum of the fuselage to be utilized for cabin space. Also, having such highly isolated engine nacelles would provide low wave drag coefficients allowing for smooth and efficient flying at higher Mach numbers. The engine is quite large for the aircraft and because mounting engines aft on a small plane, and because it is too low to mount below the wing, it is probable that it was the only location to place the engine without making considerable compromises otherwise.
[Edit] Running a CAD model of the Hondajet through a flow sim, the upward pylons should also provide extra yaw moment stability.