There is a difference between 'off-center' and 'not in a geometric pattern'. The engines are not off-center. The axis through the 2 core engines just does not line up with the boosters.
Why not a cross pattern at 90º: because there is no reason to do so.
The core engines are placed to provide a thrust vector that goes through the center of mass.
The boosters are also placed to provide a thrust vector that goes through the center of mass. So the rocket is balanced in both phases of flight (before and after booster separation).
This is not the only launcher that does not line up all engines in a regular pattern:
(image from the F9 user manual) This is the coordinate frame for the Falcon 9. The 8 engine bells are rotated a bit in relation to the Y and Z axes.
The strongback is in the +Z direction. In a Falcon Heavy, the 3 cores are along the Y axis, so the FH is not symmetrical around the XY plane.