The crime of apartheid under international law only looks at existing regimes and whether they apply oppression along racial lines. It does not include provisions on historic oppression done by the ancestors of the currently oppressed. That would be ridiculous.
So saying: “But they did it to a different people, dozens of generations ago” is not admissible as a justification for the crime of apartheid for the ICC. In fact the crime of apartheid has no clauses for any justification, at all, under international law.