I think you're probably right, but your counterexamples don't really refute the strongest reading of the thesis. The military establishment has always ultimately held the reins in Pakistan, so the dynamic of civilians avoiding threats by rewarding incompetence isn't there - the threat is present anyway and the rewarding isn't in their power. Afghanistan and Chechnya are confederations of tribal warlords, so of course the armed forces are controlled by competent fighters, it's almost a tautology. You need an example where there's a strong civilian central authority that controls the military effectively, and maintains a highly competent military, and isn't constantly troubled by the threat of coups.

A bit tough to do when almost all Islamic-majority countries are located in Asia or Africa, where they're prone to dictatorial tendencies and nepotism runs galore. But the few European ones are doing alright - Albania, Bosnia, Kosovo, heck might even argue Turkey (people outside Istanbul voting for Islamist Erdogan is still democracy in action).