I understand that it would be a brutal war, but even the Nazis weren't insane enough to genocide pretty much the entire population of Europe as you speak. And especially not in a life or death war against the Allies. 50 million is already a huge number for Europe, 500 million is just outright insane. Remember, the population of Europe at the time was only around 400 million.
Like, where do we even get the numbers to kill to reach that number here?
So, okay, I understand that Eastern Europe is not going to have a good time. The Nazis were all about their plans to move or exterminate the Balts and Slavs and repopulate the territory with German settlers. It would be brutal, but remember - this is still WW2 we are talking about. Germany could not spend as much resources as it wanted to for mass extermination, and Eastern Europe would just become a massive resource sink. The Nazis were horrible, but they weren't cartoonishly evil, they'd realize that slaughtering everyone while the Allies are pushing at them from all fronts is just not economical. Still, I'd place Generalplan Ost at 80-100 million casualties, and even that is a high estimate due to the reasons above.
The Nazis had no plans for mass exterminating Frenchmen, Englishmen, Benelux inhabitants, Scandinavians or fellow Germans, so any atrocities against them would be against localized resitstance groups and opposition and not a mass killing of everyone who disagrees with the Nazis as you say. Again, they're not a cartoon villain. I place deaths due to European resistance to 10 million at most.
The Holocaust will be much worse, of course, around 20-30 million. This includes not only Jews, but also Roma, homosexuals and other ethnicities that don't fall under the Generalplan Ost umbrella.
The military deaths will be much worse, for obvious reasons, but they can't go to hundreds of millions because, well, common sense applies. I'd say 50 million deaths at most, which includes collateral civilian damage.
Now, after such a war, Europe will be ruined, completely, and never stand up again, but even with the highest possible death rates, I just can't see it becoming a mass European genocide as you say.