Historically, there have been ties between Germany and Russia for a long time, through trade (eg Hanseatic League) and politics (since 1762, and especially during the Napoleonic Wars); this only deteriorated towards the end of the 19th century when Russia aligned with France against Germany and Austria-Hungary.
I would see McMaster's use of unnatural based on several aspects, some of which have already been mentioned:
The 1914 split into social democrats and communists, with the latter attacking the former as 'class traitors'. Since they were aligned with the Soviet Union after the Russian Revolution, there is a natural antipathy against the USSR on the side of the social democrats. After all, they are the friends of their enemies.
Later developments in the USSR turned it into a dictatorship under Stalin, which was communist only in name. The German right had (temporarily) no qualms aligning with the USSR for short-term political goals (dividing Poland) in the 1939 treaty. The attack on the USSR in 1941 was then the implementation of the fascist 'Lebensraum' policy. At this point, the social democrats are out of the picture, being either in exile or in camps. But Stalinism is also counter the social democratic view — again it would have been unnatural for there to be any affinity towards the USSR.
Post-war, the SPD in the East was coerced to join with the KPD (communist party) to form the SED. This was not what many social democrats would have wanted. When in power, Brandt's Ostpolitik tried to accept the historical developments and aimed for reconciliation with Poland especially. Many (especially younger) social democrats were not impressed with what they saw as American imperialism and had some sympathies for the USSR, but often also saw the negatives (and that it was essentially a dictatorship, not a communist society). I think that is the one aspect where any affinity originates from.
With the collapse of the USSR post-1991, it turned into an oligarchy where a small elite was plundering the wealth of the country, and despite initial hopes Russia did not turn out as a western-style democracy. A repressive pseudo-democracy is not what social democrats would support, so this again would be unnatural. Even with America behaving somewhat erratically with Bush jr (Iraq war) and later Trump, most social democrats would probably still take the side of the US if pressed, as it is at least somewhat more democratic.
I think McMaster's use of unnatural affinity is based on a pro-American world view (what else would you expect from him?). While the USSR/Russia has never really been anywhere near a political system that social democrats would view as desirable (at least in hindsight with more information available — not sure how much people knew at the time), the main reason for any affinity was the duality between the US and the USSR during the Cold War, when US imperialism was seen as more of a danger to World Peace than the USSR, which mainly kept to itself (unlike during the immediate post-war era).
Gorbachev eventually agreed to German re-unification.
I still remember vividly that Yeltsin (as mayor of Moscow) was seen as a hero when he defeated the coup in August 1991; and the perception in the mid-80s was that the USSR supports existing governments/regimes (eg in Cuba, Afghanistan), while the US actively tries to topple them (eg Cuba, Nicaragua, Vietnam). While the KGB murdered individual dissidents, the CIA was engaged in wholesale regime-change.
It has been a slow process to accept the harsh reality, which makes it even more remarkable how quickly Germany acted in the face of the Russian invasion of Ukraine. WWII still looms large over any military thinking in Germany.
Someone like McMaster would have a different view of these events, and thus find it hard to understand why there was any logical reason for pro-Russian sentiments in Germany.
(Note: I grew up in Germany in the 1980s, so a lot of this is based on my personal experiences; I do accept that other people have different views on what the perceptions were at the time.)