First, the claim that Windows became a popular target platform because DOS was a popular platform before it is patently absurd. The two represent completely different programming paradigms. DOS programmers could have just as easily moved to programming the Mac as the could have moved to programming Windows. Indeed, as you point out, DOS programmers were as reluctant to start coding for Windows as they were to start coding for the Mac. Windows doesn't gain all that much by virtue of having been written to run on top of DOS. People still had to buy new hardware to start writing code for Windows.
Second, the discussion isn't about which platform is "surperior" in some way or another. It's about whether or not Apple have figured out what developers want. The fact that Apple chose Unix as the underpinnings for OS X isn't much of an indication that they have figured this out given that much of the design of Aqua still reflects much the old Apple attitude about their way or the "wrong" way to do things. Nor, for that matter, does the fact that OS X's support for Java is better than Windows' support give any more of an indication that Apple have figured this out.
And, no, I haven't accounted for the fact that the PC, indeed Windows, was the dominant target platform long before David Cutler started making foot-sized holes in the walls of Building 8. I don't quite see how it would be necessary for me to do so in order to substantiate the point.