I agree with you on several regards. I certainly agree with you that Germany cannot be claimed as a whole. Certainly certain states were treated better than others. Bavaria for instance was Napoleon's ally for the whole war up until 1813 (and N was the father in law of Bavaria's king's daughter- well adopted father in law). Napoleon treated Prussia pretty rough as well as Westphalia. Saxony was probably treated worse by the Allies in 1813 than the French.
I am not trying to play a blame game here. You are correct many of Napoleon's troops were allies and not his own and treated people badly. The French did in France under Soult in the south. The fact of the matter is that you have tens of thousands if not hundreds of thousands of guys walking around with guns, swords etc. If they are hungry they will do bad things to fill their bellies. Whether that came from the top is a different story, but it is an undeniable fact of war.
Dwyer's books certainly had an anti-Napoleonic tinge to them. His statistics that I mentioned earlier however were cited, but in a foreign language. I would love to read them myself to get the scoop but cannot. therefore I cannot tell if he cherry picked numbers. However every historian I read has an agenda regarding Napoleon to paint him as a devil or a savoir, so virtually every book on Napoleon regarding "grey" issues needs to be taken with a grain of salt.
My final point, N, even if we use the most damning evidence against him, was not the creator of such policies. Louis XIV burned the Palatine down in 1689 in a systematic way that has few parallels even in the 20th century. Frederick the Great parked 100,000 Prussian troops in Saxony for nearly seven years and sucked everything he could out, both in men and money (I saw one source that stated that Saxony's population dropped by 100,000 during Frederick's occupation). The French were bruts in the Seven Years War as well not to mention the Russians and Austrians. So N was only following the fine examples put forth to him by his enemies in former times...