Consciousness is the most recent module, and that does mean [that drawing causal arrows from consciousness to other modules of human mind design is ruled out, evolutionarily speaking.]

The causes of the fixation of a genotype in a population are distinct from the causal structures of the resulting phenotype instantiated in actual organisms.

First comes allele A, which is advantageous of itself, and requires a thousand generations to fixate in the gene pool. Only then can another allele B, which depends on A, begin rising to fixation.

That doesn't sound right to me.

First, fixation is much faster. The earliest known DNA sequence with the lactase tolerance gene is 4300 years old. That's less than 200 generations ago and the gene looks to me to be quite fixed in the Northern European populations.

Second, allele B can piggyback. Allele A spreads through children of allele A carriers. If some subpopulation of A carriers also has allele B, their children will also have both A and B and these children have even more of an evolutionary advantage than children of just A (but not B) carriers.

Sorry, but no.

Yes, maybe some very similar forms of all the other modules which can still be found in our human mind design today were necessary for consciousness to arise. But this does not mean that the modules which are actually there now could not have evolved out of these modules because they work better for a conscious agent.