I don't see how you can achieve a reductionist ontology without positing a hierarchy of qualities. In order to propose a scientific reduction, we need at least two classes, one of which is reducible to the other. Perhaps "physical" and "perceived" qualities would be more specific than "primary" and "secondary" qualities.

Regarding your question, if the "1->2 and 1->3" theory is accurate, then I suppose when we say that "red is more like violet than green", certain wavelength ranges R are causing the human cognitive architecture to undertake some brain activity B that drives both the perception of color similarity A a well as behavior which accords with perception C.

So it follows that "But, by definition of epiphenomenalism, it's not A that causes people to say the above sentences S1 and S2, but rather some other brain activity, call it B." is true, but "But now by our theory of reference, subjective-red is B, rather than A." is false. The problem comes from an inaccurate theory of reference which conflates the subset of brain activities that are a color perception A with the entirety of brain activities, which includes preconscious processes B that cause A as well as the behavior C of expressing sentences S1 and S2.

Regarding S2, I think there is an equivocation between different definitions of the word "subjective". This becomes clear when you consider that the light rays entering your eyes are objectively red. We should expect any correctly functioning human biological apparatus to report the object as appearing red in that situation. If subjective experiences are perceptions resulting from your internal mechanisms alone, then the item in question is objectively red. If the meaning of "subjective experience" is extended to include all misreportings of external states of affairs, then the item in question is subjectively red. This dilemma can be resolved by introducing more terms to disambiguate among the various possible meanings of the words we are using.

So in the end, it still comes down to a mereological fallacy, but not the ones that non-physicalists would prefer we end up with. Does that make sense?

This is an interesting example, actually. Do we have data on how universal perceptions of color similarities, etc. are? We find entire civilizations using some strange analogies in the historical record. For example, in the last century, the Chinese felt they were more akin to Russia than the West because the Russians were a land empire, whereas Westerners came via the sea like the barbaric Japanese who had started the Imjin war. Westerners had employed similar strong arm tactics to the Japanese, forcing China to buy opium and so on. Personally, I find it strange to base an entire theory of cultural kinship on the question of whether one comes by land or sea, but maybe that's just me.