Allohistorical Allusion: One rather subtle difference is that just as you start to wonder why "President Kennedy" is still alive and acting so Out of Character, the realisation dawns that America elected former ambassador Joseph Kennedy, JFK's father.
Animal Motifs: Xavier is compared to a fox by the narrator, who also says that he doesn't run with the (wolf) pack. (And groups of submarines are also called wolf packs. Xavier and Max were on subs during World War 2.) Max is compared to a bear.
Asshole Victim: Doesn't get much worse than the people who engineered the Holocaust.
Brainwashed and Crazy: What March actually thinks of his son educated by the government, although he pretends to be proud of him.
Can't Stop The Signal: Very ambiguously done; we only see what the main character is believing to be happening, not what is actually happening.
Crapsack World: For Detective Xavier March, it most certainly is. Divorced? Check. Son hates you? Check. Nightmares? Check. PTSD? Check. Living in apartment previously owned by Jewish family, who were "sent East"? Check. Suddenly discovering that the regime you serve is full of mass murderers? (You see where this is going, right?)
Also for anyone who doubts or differs from the Party line on any of a thousand things. For example, we see a priest whose church is across the street from police HQ, in a regime which officially discourages religions other than Hitler-worship. He is not a cheerful-looking man.
Deconstruction: Of previous "Hitler wins the war" scenarios. Germany in 1964 is not a very nice place by any means, but rather than the 'the Nazis take over the entire planet' scenarios common to the sub-genre, it's clearly ended up as closer to being an analogue of the Soviet Union than an all-powerful unstoppable juggernaut. German territorial expansion is limited to the East, as planned in real life, while the nations of the west are clearly satellite states more-or-less subservient to German hegemony but nevertheless independent from direct German control (again, as planned in real life). Rather than invading the United States and conquering it, there's a Cold War between them which is starting to warm into an uneasy detente, and rather than the Thousand Year Reich lasting forever and ever it's implied that Germany is slowly beginning to stagnate and will ultimately collapse from within anyway.
For Want of a Nail: The Allohistorical Allusion mentioned above might seem like a minor detail, but it may be a hint at the story's "point of divergence". When Joseph Kennedy was ambassador to Britain he was strongly in favour of appeasement with Germany well into 1940, and lost a lot of public face because of it. In this timeline, although America still clashed with Imperial Japan, it stayed out of the war in Europe.
Heroic BSOD: While reading secret documents, Xavier comes across a real historical note about concentration camp victims' hair being cut off and turned into felt, which was then made into socks for U-boat crews. He reacts badly to the news that he wore dead Jews' hair during the war.
Hope Spot: Near the end of the book, after March has been horribly tortured by Globus, it appears that Arthur Nebe, Krebs and Max Jaeger have planned his escape so he can reveal the truth about the Holocaust to the world. However, March quickly deduces that they are trying to trick him into leading them to Maguire.
In Spite of a Nail: Played with; the English rock-and-roll band who are often mentioned as becoming increasingly popular with the youth are never explicitly named, but it's pretty clear that they're either supposed to be The Beatles or an alternate universe equivalent who are close enough to them to make no real difference.
Nazi Protagonist: Averted. Despite holding the SS-rank of Sturmbannfuhrer (which equates roughly to Major in the Wehrmacht and Komissar in the pre-Nazi Germany police force), it's mentioned several times that, despite being a very capable investigator, the protagonist hasn't progressed further in his career because of his outright refusal to become a party member. It's why he has such a poor relationship with his ultra-Nazi son and ex-wife and one of the main reasons that the kid betrays him.
Shell-Shocked Veteran: Protagonist Xavier shows occasional signs of this, which might have contributed to the breakdown of his marriage. Living through the war certainly left him with a much-diminished view of the Third Reich.