Good point on the solo cup approach to making some pollen. If I try reversing this winter, I will likely do exactly that - an initial grow in very small containers, collect and store the pollen, then on to the proper grow and careful pollenation of a few lower branches of the seed makers. If anything, it will add to the winter pandemic entertainment, and I may end up with some useful seeds.
You also make a good point about even great breeders still finding phenotypic variation in established strains. Bottom line is that you can never get rid of it all. There are thousands of genes, many with recessive variations, many of the characteristics we are interested in are controlled by multiple genes, and expression of many of the genes are probably switched on and off by environmental conditions, or the actions of other genes. Reality here is deeply complex, and we just get to see the surface results.
The best breeders concentrate on the important objectives for a given strain - autoflowering consistently, taste, potency for examples, and weed out the mischief in these specific objectives as best they can to produce strains that behave themselves with reasonable predictability. In spite of this, some phenotypic variation is impossible to avoid. After all, Mother Nature still produces it after millions of generations of natural selection. Our little breeding efforts to F5 or so are trivial by comparison.
Mephisto Genetics is one of the good breeders, and reading their descriptions of their breeding efforts for individual strains is an entertaining window to how this stuff gets done well.
Good luck with your breeding.