True: depending on the parameters of a particular market, things may go one direction or the other. I acknowledged as much in the footnote referenced in the part you quoted, and indeed gave a scenario where the input prices go in the opposite direction as profits!
So your theory [1] would require that this "make everyone a better programmer" is more like wage-fixing (in terms of economic incidence) than the tomatoes, even though
a) the wage fixing affected demand, and this education program affects supply, of programming labor; and
b) the big companies are a much bigger fraction of the SV labor market than of the workers that would learn through this program.
It's also not clear to what extent the wage fixing agreement was mitigated by driving programmers to non-conspirators.
Getting the full picture would require a careful assesent to the sensitivity of these markets to all those parameters, not simply assuming that any increase in the supply of programmers purely benefits employers of them and doesn't affect the relative scarcity of their final output.
And FWIW, I don't get your insistence that one theory requires "perfect competition"; it might require some level of competition, but why perfect? The tomato result would hold true even in very lumpy markets. (Or were you just exaggerating?)
[1] I know, not "your" theory, but it's much simpler than "the theory you offered in your previous post", and I add this footnote only to fend off a possible indignant reply about "hey, that's not just my theory".