Part 1

Most of them were just soldiers fighting a war they didnt wanna be in, right?

Not really. It's a fair assertion to say that virtually all Wehrmacht soldiers were aware of the atrocities that were committed, participated on some level in these atrocities and viewed most of it as legitimate.

I have previously wrote answers to similar questions here, here, and here and it is not really possible to gauge the number of how many members of the Wehrmacht were directly involved in war crimes, not at least because the difficulty of establishing what "directly" means in this context: E.g. was a group of soldiers guarding an Einsatzgruppen mass shooting directly involved or not?

The question of how many knew of war crimes and what they knew of them is easier to answer, especially in light of the newer research by Felix Römer as well as Sönke Neitzel and Harald Welzer. They worked extensively with Allied protocols of conversations between German POWs recorded in Allied camps when they didn't think anybody was listening. Their research uncovered that knowledge of war crimes was ubiquitous among members of the Wehrmacht. Every soldier knew of atrocities that had been committed against Jews and other civilians because they had either been present, had participated or had been told about them by their comrades. During their time as POWs, they quite freely discussed these crimes. To exemplify this, Römer cites among others the following exchange between the Viennese Artillerie-Gefreitem Franz Ctorecka and the Panzer-Gefreiten Willi Eckenbach in August 1944 in Fort Hunt (translation my own):

C: And then Lublin. There is a crematoria, a death camp. Sepp Dietrich is involved there. He was somehow caught up in this in Lublin.

E: Near Berlin, they burned the corpses in one of these thingies ["einem Dings], the people were forced into this hall. This hall was wired with high-voltage power-lines and in the moment they switched on these lines, the people in the hall turned to ashes. But while still alive! The guy who was in charge of the burning told 'em: "Don't be afraid, I will fire you up!" He always made such quips. And then they found out that the guy who was in charge of burning the people also stole their gold teeth. Also other stuff like rings, jewellery etc.

[Römer, p. 435f.]

What this passage shows is that these Wehrmacht soldiers, who after all were both on the lower side of the ladder, being only Gefreite (lance corporals) were uncannily well informed even if the story about using electricity for executions wasn't true. But knowing not only of the Majdanek death camp near Lublin but also knowing about Sepp Dietirch's involvement proves them to be very well informed.

Or take this exchange between two Wehrmacht soldiers, Obergefreiter Karl Huber and Pioniersoldat Walter Gumlich, in Fort Hunt:

H: One day, one guy just came and stole this Russian's cow and so the Russian defended himself. And then we had to hang fifty or a hundred men and women and let them hang there for three or four days. Or they had to dig a trench, line themselves up at the edge and were shot so they fell backwards into it. Fifty to a hundred people and more. That were the so-called "retributions". But that didn't help anything. Or when we set the village son fire [...] Partisans were naturally dangerous, we had to defend ourselves against them but this was something different [...]

G: Ach, that were war operations. They [the people who did the above] are not really criminals.

H: Exterminating whole families, shooting their kids etc., literally killing whole families? We are guilty if the military without any right or any order steals the last bread of some farmer.

G: Oh, come on.

H: Ach, don't defend them.

These and so many more conversations of this kind between Wehrmacht soldiers show that virtually every soldiers had either heard or seen these crimes if he had not participated in them himself. And given how numerous the crimes of the Nazis and the Wehrmacht were in the Soviet Union and elsewhere, this is hardly surprising. You already mentioned it in your expanded text above and I go into this in the linked answers but it is imperative to realize that the war against the Soviet Union was planned, conceptualized and fought as a war of annihilation, being in itself basically a huge war crime. Nobody is this fact more obvious than in the OKW's Kriegsgerichtsbarkeit Erlass, which actually forbid Wehrmacht soldiers from being persecuted for war crimes in the Soviet Union. That this was seen as necessary, tells you not just how deeply the Wehrmacht was involved but just what kind of war they planned to fight: One where combat operations and war crimes bled into each other seamlessly.

The background of this is touched upon in my linked answers as well as by Dr. Waitman Beorn in the linked AMA here.

Now when it comes to the question of rationalization, the protocols reviewed by Römer et. al. are also rather enlightening. As you might have noticed in the converstaion between Huber and Gumlich above, these crimes were sometimes regarded as controversial. Römer in his analysis proposes based on the protocols that Wehrmacht soldiers did indeed distinguish between what they viewed as legitimate and illegitimate violence.

Take this exchange Römer cites between soldier Friedrich Held and Obergefreiter Walter Langfeld about the topic of anti-Partisan warfare:

H: Against Partisans, it is different. There, you look front and get shot in the back and then you turn around and get shot from the side. There simply is no Front.

L: Yes, that's terrible. [...] But we did give them hell ["Wir haben sie ganz schön zur Sau gemacht"],

H: Yeah, but we didn't get any. At most, we got their collaborators, the real Partisans, they shot themselves before they were captures. The collaborators, those we interrogated.

L: But they too didn't get away alive.

H: Naturally. And when they captured one of ours, they killed him too.

L: You can't expect anything different. It's the usual [Wurscht ist Wurscht]

H: But they were no soldiers but civilians.

L: They fought for their homeland.

H: But they were so deceitful...

[Römer, p. 424]

Römer uses this exchange to illustrate that even where there was a limited understanding for the Partisans and those who helped them (fighting for their homeland), as irregulars, they neither got nor deserved mercy. The Partisans were constructed by the Wehrmacht as dangerous, deceitful, and likely to shot them in the back. Violence against them and against civilians in general were justified and rationalized with this. Within this frame of reference, a lot of the most extreme violence committed by the Wehrmacht in occupied Europe was justified and for the soldiers, this view seemed natural and justified. They used it to justify and describe the most extreme atrocities and discussed them not as problems but rather with satisfaction. Fritz Kotenbeutel, a 24-year-old Wehrmacht soldier of an anti-Partisan unit speaks with great satisfaction of the good job they did burning down villages and executing every male they came across [Römer, p. 428].