Yockey is somewhat inconsistent, in that he makes clear that Negroes and Chinamen can never be Westerners, and although he cites "culture" for the Chinaman, he does mention physical differences for the Negro.
While some speculate that Yockey's opinions on this topic were formed by his ancestry (Jewish blood?) or the influence of Spengler, another, probably more likely, explanation that is compatible with the above mentioned inconsistencies, is that Yockey was focused on intra-European racial differences.
One must remember when Yockey was writing, and that, while today, most people use "race" to mean the major continental population groups, in the past, there was much talk about the "Nordic" and "Alpine" and "Mediterranean" "races" of Europe. Indeed, it was sometimes customary to talk of the "English race" or other "races" constituting what most today would call ethnic groups (of course "race" boundaries can be somewhat subjective - race or subrace? - and one can use "ethny" to denote various levels of biological differentiation).
Further, the "Nordicism" or "Germanism" or "Aryanism" of the National Socialist regime was fresh in everyone's mind when Yockey wrote Imperium, and Yockey directly critiques "materialist" National Socialist race theory. The following quote from Imperium is instructive as to Yockey's probable motivation:
The touching of this racial-frontier case of the Negro
however, shows to Europe a very important fact
— that race-difference between white men, which means Western men, is
vanishingly small in view of their common mission of actualizing a High
Culture. In Europe , where hitherto the race
difference between, say, Frenchman and Italian has been magnified to great
dimensions, there has been no sufficient reminder of the race-differences
outside the Western Civilization. Adequate instruction along this line would
apparently have to take the form of occupation of all Europe, instead of only
part of it, by Negroes from America
and Africa , by Mongols and Turkestani from the
Russian Empire.
Thus, I suspect that Yockey was primarily focused on "race" in its narrower aspects, and took for granted that people would understand the physical differences between Europeans, Africans, and Asians. On the other hand, Yockey was concerned that an emphasis on "racial materialism" would damage the Western unity he so desperately wished to foster.
Perhaps Yockey could be excused given he wrote Imperium before the discovery of DNA and didn't have access to today's knowledge, especially the Salterian idea of Ethnic Genetic Interests. The Yockey "problem" can be 'solved" by acknowledging the biological differences that exist within Europe, and that these need to be preserved, but that these differences are small in the global context, and need not impede the Western Unity that Yockey recognized is all-important.