The theme of this post isn't very accurate, as large phenotypic polymorphisms in various other species demonstrate - e.g.:

From a strategic point of view we are especially interested in those species that have two kinds of males. It's almost like having a third sex. In fact the winged males look far more like females than they look like wingless males. Both females and winged males are almost believable as wasps, although they are tiny. But the wingless males are nothing like wasps to look at. Many have savage pincer jaws which make them look a bit like miniature earwigs going backwards. They seem to use these jaws only for fighting — lacerating and slicing to death other males that they encounter as they stalk the length and breadth of the dark, moist, silent garden that is their only world. - Climbing Mount Improbable, Richard Dawkins.

Where did the reasoning go off the rails?

It isn't just the case of males and females where different alleles can form a truce. There's the whole phenomenon of frequent-dependent selection. Most people are familiar with this from blood types, and sickle-cell anaemia. Alleles with phenotypic effects involving disease resistance can be advantageous when rare and disadvantageous when common - resulting in them never going near extinction or fixation.

Also, this premise is inaccurate:

If gene B depends on gene A to produce its effect, then gene A has to become nearly universal in the gene pool before there's a substantial selection pressure in favor of gene B.

Gene B can spread if gene A is present at a frequency of 20% in the population - provided it is not deleterious in the absence of gene A. Sure, then the selection pressure maintaining it is reduced by a factor of five, but that's not necessarily enough to kill it off.

Finally, phenotypic variation does not necessarily depend on genetic variation. There's also the influence of the environment to consider. In general, the environment is quite capable of sending some organisms down different developmental paths depending on the circumstances in which they find themselves. This is known as phenotypic plasticity.

There are plenty of examples of phenotypic plasticity in humans - e.g. the effect is an important part of the reason why a Sumo wrestler and a racing jockey have different phenotypes.