Nightlily said:
Depends on when you start your seeds - if you force plants to grow earlier (inside, under lights) they will have to acclimatize to natural conditions. The same here if I get plants from Northern Germany or Italy. Takes them sometimes 2 years to flower in time.
I have no idea if a GA-treatment changes something in the plant that works 'forever'. But I tell you a story about tissue culture and daylilies. There are only a few commercial sources for daylilies within the EU and I know 2 of them that propagate their plants with tissue culture (usind a lot of plant hormons, special fertilizers, ...).
I have plants from both sources here in my garden - they did grow well at the producers place, were sold in small clumps (2-3 fans) and they flowered as they should here in my garden the first year.
These plants are now more than 5 seasons in my garden - only 1/2 of them performs normally (growth, bud count, ...); 1/4 flower but do not grow - still 2-3 fans and 1/4 do not flower every year and do not grow either.
One of the sources is a friend of mine - does the tissue-culture propagation on a small scale in his nursery. He told me, that he has to cull a certain amount of plants because they show flaws - and sells only the ones that look like they should. Invisible 'flaws' like weakness in growth are completely hidden by the artificial treatment - so I would assume that this could also happen if you dope your seedlings. 
I have read about the TC stuff from meristems (I think). I do think there that the epigenetics can indeed change leading to a permanent change in gene expression in some cloned plants (obviously the genetics are identical to the parent plant, unless it was a revertant back to diploid from tetraploid conversion). So, yes, colors can be off as well as all the other factors you describe. But the pollen should still be good-to-go as the original, for further crosses (as epigenetics are supposed to be reset in gametes). But the seedlings I describe are allowed to naturally establish prior to a transient treatment. Far less harsh.
I think the only way if you really wanted to know would be to take a small number of your "for-the-bin" daylily rejects and test those. Then you have nothing to lose (aside from the all-too-precious space, of-course), and everything to gain.
I am very impressed by the seedling flowering times you observe, and I am also well-impressed by your note-taking skills on this.
I suppose, personally, I do not see the GA treatment any different to people who add diluted peroxide to their seeds to help them germinate. A foreign chemical was added to speed up a natural process. Does that peroxide doping change the daylily that arises, forevermore? I doubt it.
But, we are still dancing around hypotheticals with neither of us having a shred of evidence one way or the other. This is why I cannot answer your questions fully, as the evidence just does not exist.....yet. It is all just pure conjecture at this very early point.
These are the TC papers for daylilies that interested me, but I could not lay my hands on them as they are too old:
Krikorian, A. D., and R. P. Kann. 1979a. Micropropagation of Daylilies Through Aseptic Culture Techniques: It's Basis, Status, Problems, and Prospects. Hem. J. 33(1):44-61.
Krikorian, A. D. And R. P. Kann. 1979b. Clonal Micropropagation of Daylilies. Pp. 835-836. In Plant Cell and Tissue Culture: Principles and Applications. Ed. By W. R. Sharp, P.O. Larsen, E.F. Paddock, and V. Raghaven. Columbus: Ohio State University Press.
Krikorian, A. D., and R. P. Kann. 1980. Mass Blooming of a Daylily Clone Reared from Cultured Tissues. Hem. J. 34:35-38.
Krikorian, A. D., S. A. Staicu, and R.P. Kann. 1981. Karyotype Analysis of a Daylily Clone Reared from Aseptically Cultured Tissues. Ann. Bot. 47:121-131.
