Heydrich was content for Jews to be targeted "as Jews", and this filtered down into instructions such as the fact that, as noted in EM 10, pogroms were to be co-ordinated with "anti-Communist" and "anti-Jewish" groups. The separation of "Communists and Jews" into two categories would appear in numerous killing reports, with Jews gradually constituting by far the largest number of people who were shot. Heydrich had notified the four Einsatzgruppen leaders verbally on June 17 (confirmed in writing on June 29) that pogroms were not to be hindered when instigated by "anti-Communist or anti-Jewish circles" and that such pogroms should be "implemented", "intensified when necessary" and "directed onto the right path" (translation by William Templer). Two days later, Heydrich's Einsatzbefehl Nr. 2 made it clear he was referring here to pogroms carried out by ethnic Poles. His order was also enclosed in EM 10, shown here, preceded by the line cited above which included the revelation that this targeting had been suggested by the "17th Army Command" (presumably Stülpnagel), thereby demonstrating the extent of Wehrmacht collusion. EM 10 also included a note from Einsatzgruppe C in Vilnius that EK 7a had initiated action against "Communists and Jews." This action was subsequently handed over to EK 9, which was led by Filbert, a man fiercely devoted to Heydrich's worldview and mission.
For the Balkans, Heydrich had reached an agreement with quartermaster-general Wagner, put in writing on April 2, 1941, stating that measures against "Communists and Jews" were to be within the remit of the Security Police (OKH/Gen.st.d.H./Gen.Qu. Abt. Kriegsverwaltung, Nr.II/0308/41, cited in Heer, p.75). The Wehrmacht then fully collaborated in the shooting of Jewish hostages in reprisal measures in Serbia in the summer and autumn of 1941, leading eventually to the genocide of the male Jews, as recorded in Eichmann trial documents T/867 to T/875 and as summarized by Browning online here and by Stephen Vargas online here. This was then followed in the first half of 1942 by the murder of Jewish women and children in gas vans, as Hans shows here in his refutation of Alvarez and Mattogno.
Whereas Mattogno and Graf claim that a policy of "emigration" was still being pursued by the Germans in the autumn of 1941, the research of Anderl and Manoschek has shown that the shootings of men and gassings of women included Jews who had tried to reach Palestine in late 1939 but become stranded in Kladovo, Serbia. Those Jews were buried in a site in Jajinci, which was exhumed and investigated by the Yugoslavs in documents available here, corroborated by testimonies such as that of a Yugoslav who had been forced to dig up and burn bodies (translated into English here). At the very least, this shows that, as of October 1941, the Germans were not pursuing Jewish emigration but were rather placing non-Soviet Jews in positions where they could be used as hostages for reprisal measures and also "parked" in places such as Lodz, decimating them through overcrowding and labour while awaiting the opportunity to kill them farther east in the wake of the Jews who were already being exterminated there. Meanwhile, extermination by shooting was taking place in eastern Galicia, most notably Bloody Sunday, as described by Pohl here. As Nick Terry notes here, Einsatzgruppe z.b.V. had already executed at least 19,338 people by September 9, 1941.
The Wehrmacht's approval for such measures can be gleaned from the statements of its own commanders, collated and analyzed here and here and here and here and here. Mattogno and Graf's claim that many other eastern Jews were killed only "on account of sabotage, anti-German activities, as carriers of diseases, and above all as retaliatory measures for partisan attacks" is also refuted in those links, which also provide sufficient material to forewarn any unwitting reader that Mattogno's forthcoming Einsatzgruppen study will not take denial any further forward as a plausible contribution to scholarly understanding of these issues.