Firing takes place near top dead center. With a shared crank pin, if the V-angle is 90 degrees then only one piston will be at TDC, while the other is leading or lagging by 90 degrees (mid-stroke).
If you split the crank pins by 90 degrees you can have both pistons at TDC center at the same instant in crank rotation. If your V-angle is 45 degrees, split the crank pins by 45 degrees to match.
Split rods or side by side don't make a difference here, other than a split rod won't work on two crank pins 90 degrees apart...
It sound like you are aware a 2-stroke needs both pistons at DTC together for crank case compression.