That's measuring different things. We can tell whether a particular copy of a gene came from the Neanderthal gene pool or the main SSA gene pool by looking at its sequence (esp. at SNPs), but the overall base pair sequence of that gene will still be 99.9% the same.

When we say that chimpanzees and humans share 99% of their genome, we're looking at base pairs, but when we say that modern Eurasians have 1-4% of their genome from Neanderthals we're looking at genes.