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The separate status of Crimean Karaites during the Nazi era clarifies it was all about race:
https://en.wikipedia.org/wiki/Crimean_KaraitesIn 1934, the heads of the Karaite community in Berlin asked the Nazi authorities to exempt Karaites from the anti-Semitic regulations based on their legal status as Russians in Russia. The Reich Agency for the Investigation of Families determined that, from the standpoint of German law, the Karaites were not to be considered Jews. The letter from the Reichsstelle für Sippenforschung (de) officially ruled:The Karaite sect should not be considered a Jewish religious community within the meaning of paragraph 2, point 2 of the First Regulation to the Reich Citizenship Law. However, it cannot be established that Karaites in their entirety are of blood-related stock, for the racial categorization of an individual cannot be determined without … his personal ancestry and racial biological characteristicsThis ruling set the tone for how the Nazis dealt with the Karaite community in Eastern Europe. At the same time, the Nazis had serious reservations about the Karaites. SS Obergruppenfuhrer Gottlob Berger wrote on November 24, 1944:
"Their Mosaic religion is unwelcome. However, on grounds of race, language and religious dogma... Discrimination against the Karaites is unacceptable, in consideration of their racial kinsmen [Berger was here referring to the Crimean Tatars]. However, so as not to infringe the unified anti-Jewish orientation of the nations led by Germany, it is suggested that this small group be given the opportunity of a separate existence (for example, as a closed construction or labor battalion)..."Despite having exempt status, groups of Karaites were massacred in the early phases of the war. German soldiers who came across Karaites in Russia during the invasion of Operation Barbarossa, unaware of their legal status under German law, attacked them; 200 were killed at Babi Yar alone. German allies such as Vichy France began to require the Karaites to register as Jews, but eventually granted them non-Jewish status after getting orders by Berlin.
When interrogated, Ashkenazi rabbis in Crimea told the Germans that Karaites were not Jews, in an effort to spare the Karaite community the fate of their Rabbanite neighbors. Many Karaites risked their lives to hide Jews, and in some cases claimed that Jews were members of their community. The Nazis impressed many Karaites into labor battalions.
According to some sources, Nazi racial theory asserted that the Karaites of Crimea were actually Crimean Goths who'd adopted the Crimean Tatar language and their own distinct form of Judaism.
Karaim cemetery in Warsaw, established in 1890.
Karaim cemetery in Trakai.
In Vilnius and Trakai, the Nazis forced Karaite Hakham Seraya Shapshal to produce a list of the members of the community. Though he did his best, not every Karaite was saved by Shapshal's list.