Some of my reading seems to suggest that the shutdown threshold is the entire cause of the strength deficit, yet a distinction is made between it and levels of muscle activation.
Can somebody's shutdown threshold be above what their muscle activation would allow (thus not stimulating it)?
Can somebody's shutdown threshold be below what an athlete's muscle activation would normally have allowed?
I think you are misinterpretting the shutdown threshold. The shutdown threshold is just the point at which the golgi relfex says no more, and won't allow the firing rate to increase or for you to recruit more motor units. It's a safety mechanism to prevent injury, and getting stronger is largely about increasing this threshold by making the body comfortable with heavy weights. This reflex can also take place due to an extended time under tension, for example while doing isometrics (this is one of the principles of PNF stretching).
So really, your maximum level of muscle activation (measured in MU recruited and firing rate) is really the maximum level that your golgi reflex is allowing.
They are the same thing, and really both terms are just ways of making people think physiologists know more than they really know ;-)
Is this where the idea of negatives came from? the old school timed reps? Where it may take an 8 count to bring the weight down then you blow the weight back up then repeat? was this the reason we use to do those?