I don't know about ecu counting the time since last clutch pull.
Here are some of the reasons I do know why we use less fuel on long cruising rides compared to short runs.
More fuel used below certain rpm for as long as you have the clutch pulled. That adds up waiting in 1st gear on the light or in stop & go.
Low oil temp increases injector time. Takes a while to get up to operating temps, in the cold we hardly even get there
Starting signal causes longer injector time.
Acceleration signal (throttle) increases injector time. On a long cruise we are less likely to let it rip.