One thing to remember, and you may already know this, is that your armies are never without a leader. A "default" gets assigned with the following traits:
Shock: -1
Defense: -1
Morale: -1
Organization: -10
Reliability: -1
Speed: -10
Fire: -1
Experience: -25
I remember reading somewhere that native divisions have a lowered reliability. This could be true of divisions built from pops other than your nationals as well, but I am unable to locate anything in the files to confirm this. Of course, I had to use the pop-up tool tip over the default leader to get his stats, since it appears to be hard-coded in the game. Lowered reliability of native and non-national divisions must be hard-coded as well, assuming that is the case. We can probably confirm this by going into the detail screen of regular, native, and non-national divisions; but I can't do that right at this moment.
One question in my mind now. Is there any correlation between unit reliability and soldier pop militancy? My guess at the moment is no, because of the differences in the revolts. One involves an actual division revolting, while the other is another case of revolters created (sort of out of nowhere) from a disaffected pop.