Stephen Gray's article on the P-38 in Pilot (June 1995), mentions that 'opposite' propeller rotation was tried in an effort to eliminate control problems at high (diving) speeds, due to compressibility.
However it is not clear whether this is 'opposite' in the sense opposite to the normal P-38 rotation as described at the start of the thread, or opposite to the 'normal' rotation on most twins. Regardless of the sense, the change didn't cure the control problems.
But, if they tried opposite sense prop rotation to cure the control problems and found that this had other benefits, even through they didn't cure the control problems, they may have left the engines in this 'odd' configuration.
Stephen's article doesn't give any hints as to the reason for the 'odd' rotational arrangement.