Playing around with the Schmidt Engine Designer a bit more yields:

below 87% runner flow efficiency you get NaN crash

since this program 'forces' you to use their 'optimum' settings, I had to input all these Schmidt settings into the PerformanceTrends program to compare them.

Setting the Schmidt Engine Works program up with Magnum cylinder head flows of
208 cfm at 0.48 lift intake
171 cfm at 0.406 exhaust
and then forcing the Performance Trends EA 3.2B program to use the other settings
(like different camshaft and header dimensions)
that the Schmidt insisted on using,
the 'apples to apples' comparison is:

Schmidt predicts maximums of:
317 hp at 4420 rpm
357 ft-lbs at 3280 rpm

Performance Trends EA 3.2B program predicts for the same rpms as above:
312 hp at 4420 rpm
416 ft-lbs at 3280
Performance Trends predicts its own maximums of:
315 hp at 4300 rpm
425 ft-lbs at 3400 rpm

Looking at it this way
the only significant differences between the two programs are for max torque,
where the difference is 20%

This torque difference may be partly due to the
Schmidt Engine Works program just asking for for what it labels
'Unleaded Gasoline'
in contrast to the Performance Trends asking for an input of what AKI octane gasoline to use to calculate optimum ignition timing (93 octane was used ).