I just swapped out the flywheel, clutch and throwout bearing on my M5OD-R1HD in my Explorer, so the mechanical relationships are pretty fresh in mind.
Note: assumes all parts working correctly.
When the clutch is engaged (foot off the clutch pedal), the clutch disc is clamped by the pressure plate and turns at the same speed as the flywheel. This, in turn, means the input shaft to the transmission is turned at the same speed as the flywheel. Niether the pilot bearing nor the throwout bearing is spinning at this time. If the transmission is in neutral, you can turn off the engine and coast with no wear on the pilot or throwout bearings. They'll be stationary.
When the clutch is disengaged (foot on the clutch pedal), the throwout bearing is compressing the springs on the pressure plate, un-clamping it from the clutch disc. The throwout bearing will be rotating at flywheel speed. Any difference in speed between the flywheel and the input shaft of the transmission shows up as rotational speed in the pilot bearing. If you turn off the engine, the throwout bearing stops spinning - no wear. The pilot bearing will still be spinning, though.
In either case, if you put the transmission in neutral, the input and output shafts will soon be rotating at different speeds. Re-sycing them to get into gear will require the syncros to do work matching the speeds, unless you start the engine first and do rev-matching. If you want to bump start, you either need to leave the transmission in gear or use the sycnros.
So, for EOC, you can choose: syncro wear (trans in neutral, clutch engaged) or leg pain and throwout/pilot bearing wear (trans in gear, clutch dis-engaged). You can do leg pain AND syncro wear if you want (trans in neutral, clutch dis-engaged) but why?
If you have a Ford/Mazda M5OD-R1 or R1HD transmission, the extra wear on the pilot/throwout bearing doesn't matter: you'll probably have to tear it all apart to replace the throwout cylinder before either wears out anyway.
