Why are Stratolaunch's engines so far forward?
The forward location has two benefits:

Wing upwash is smaller, so the flow direction at the intake varies less with speed and altitude. This makes the intake more efficient and requires less robustness in its layout.
The forward location shifts the wing's center of gravity forward and gives it better flutter damping. How that works is explained here.

Wing torsion in combination with the two fuselages will produce a flutter mode where both fuselages pitch in opposite direction, torquing the center wing in the process. The slender wing in combination with the high pitch inertia of the fuselages will result in a very low flutter frequency. I suspect that damping this mode is of paramount importance for the Stratolaunch.
I also suspect that the high wing on a high fuselage allows more vertical distance between engine and wing, so the exhaust stream will pass below the lowered flaps. The high turbulence in the exhaust stream would put additional loads on the flaps; to avoid this, Boeing uses exhaust gates or a gap in its trailing edge flaps. Such a gap would not be needed with the lower engine position of the Stratolaunch. However, to place them lower does not require to shift them forward, too.