Right... I'd probably not compare two structurally different viruses to a multicellular organism like varroa. An individual can develop immunity to a virus in their lifetime but as far as we know, a bee cannot do the same for varroa so unless you're talking at a population level for the metaphor as well, I'd be cautious.
Likewise in people, treatment allowed many to develop immunity and they have more genes than just those related to covid so it helps species genetic diversity that you don't lose them because of a single weakness. 'Fitness' is not about a single trait. You also seem to conflate an anamnestic immune response with individuals with an immune system more resistant to covid and comparing to genetic resistance in bees... Not quite as simple as that really.
As for commercial producers... I think not having the cost and time cost of treatment for varroa, nor the cost of losses from it, would be commercially advantageous so I'm not sure your stance there is entirely logical.
Covid is a single stranded RNA virus. This means mutations do not get corrected like in organisms which have double stranded genetic material. As a result there are many many variants in a short time. A lot die, some persist.
Flu has building blocks of which the virus genome is composed and where multiple strains occur in an individual cell they can recombine. This does not cause new genetic material.
Variation and mutation in viruses is very different to that in multicellular organisms and even to that in bacteria. Novel mutations are usually corrected due to various mechanisms and if they are not, they need to be in the germ cells to be conferred to offspring, assuming they're not terminal to the cell involved (or like in cancer, the organism).
Most resistance traits we see developing are not novel genetics but the consequence of selection pressures increasing the prevalence or upregulating expression of pre-existing genes. It is entirely possible that certain behaviours in bees exist for another purpose but also confer advantage against varroa thus may be seen more.
Rabbits and myxomatosis... Not really. Again, caution comparing viruses and parasites. With rabbits, they get infected, many die, those that are left have immunity so aren't reinfected and the virus starts to die out as R number drops. New generations occur and have not been exposed so have no immunity, population density increases to the point R number goes up, virus spreads again and wipes out a lot of the population. And so it cycles.
The 'three choices' look to me like they have been said in hindsight. At the time it started, options one and two would be indistinguishable.
I'm not saying you don't have a point/are wrong (still mulling it over, particularly the concept of varroa becoming host adapted... Intriguing), but I am challenging the suitability of your metaphors.
