Has this engine/motec combination ever been tuned by a competent person ?
Or have you simply plugged it in with a base map and driving it like that ?
Most of the timing figures in that map are very low, right from the bottom of the table to the top. Just exactly what is the spec of the engine, how much boost, what turbo etc etc ?
Are all your sensors calibrated properly, ie MAP sensor etc ?
Your two scope traces posted look like perfectly good clean signals with no noise.
And as others have said, if there is any doubt that actual ignition timing is incorrect, you MUST verify that timing on the map refers to timing seen at the engine with a timing light.
But your ref/sync settings are correct for your age of subaru, so timing should be as commanded on the screen
As for voltage thresholds, this is explained in the webinar. At lower rpm's the voltage from the mag sensors will be lower, so they require a lower voltage threshold so they are recognised. At higher rpm's you can see from your scope trace your voltages are 10v and upwards ( albeit clipped at 10v ). So your threshold settings should be around 5v ( at these higher rpm's, not at lower rpm's ). This should eliminate any noise throwing an error