I'm not a great expert, but I think you're overemphasising the role of the 'Boers' in creating apartheid - neither DF Malan (the first apartheid Prime Minister) nor Hendrik Verwoerd was a Boer, and much postwar leadership cadre of the National Party had been educated at Stellenbosch University, which had a reputation for extremely strong Afrikaner nationalism (applying that term in the sense of all white Afrikaans speakers as opposed to merely Cape Afrikaners like Malan), which was (is) located in the Western Cape. Maybe if the Orange Free State and the Transvaal Republic had been left independent then Cape Colony and Natal would have evolved in a more 'Rhodesiaesque' direction, due to the proportionally greater influence of English speakers (who were hardly saints when it came to racial matters, as I'm sure you're aware) than in the Union of South Africa, but that's really water under the bridge.
Correct me if I am wrong, but I believe Cape Coloureds and property owning blacks in the Cape Colony had some limited degree of franchise, which was gradually removed from them post-Union of South Africa?
That, plus the Anglo population would have likely prevented the cape Afrikaner community from wielding any real degree of power. Likewise, Natal had a very small Afrikaans speaking population to begin with.
I would also wonder what the impact of the large Cape Coloured community in the Cape Colony (who, I think still are a pluraty in both the Western and Northern Cape provinces) and the Indian population in Natal would have had in a situation where the National Party wasn't disenfranchising and segregating all non-whites across the board.
