Setting aside for a moment the question of whether going from a pile of lumber to a soapbox racer really meets this definition of the issue, let me tentatively accept it as you have stated it. ;)
The point is that while the natural selection theory of somatic change is plausible for features dependent on 1 or 2 genetic bit flips (like hair and skin color), more involved features involving many more SIMULTANEOUS coding changes CANNOT BE EXPLAINED using the bit flip (or as I put it the photomorph) explanation--because it is difficult to see what the intermediate steps could be.
Ah, but here you are assuming again that there must be simultaneous changes to produce a large-scale change. But many small changes over time can just as easily - more easily, really - add up to a large change. Consider the development of eyes. Your eye is a rather complex beastie (although not perfect, as our blind spots and my glasses remind us), and were we to posit a creature with no eyes suddenly and in one fell swoop developing eyes as you and I have them, we would be quite right in dismissing that possibility as ludicrously improbable.
Fortunately, there are intermediate steps, some of which we can observe in extant creatures. Many ticks, for example, have no eyes. But what they do have are rather primitive light-sensing cells in their skin. It's not much - just enough to tell the difference between light and dark. If you think of this as a a sort of proto-eye, you can see it's an extremely simple change from total blindness. It's not a huge leap, but it is a small improvement. Telling the difference between light and dark can give you an advantage over your blind competitors, so it is selected for. If you can tell the difference between light and dark, you will be more successful and leave more offspring, and eventually your blind competitors will be driven out by dint of your superior abilities.
Now imagine a development like this millions of years ago - not hard to do, as fossilized ticks more than 90 million years old have been found, essentially unchanged from ticks of today. So then, there's a small change from blindness to the ability to sense light. And over time, many small changes of this nature continue to add up. Cells that can sense light gradually migrate over bodies to gather in one or two particular spots. Why? Well, because having one or more light-sensitive cells in the same place allows you to begin to parse out some sort of detail about the world around you - vage and fuzzy detail, to be sure, but it's still better than just knowing the difference between light and dark. So, what was just a bunch of light-sensitive cells spread all over a creature's body gradually, and in small steps, becomes a cluster or two of light-sensitive cells. And these are what are called "eye spots", and you can still see them on primitive contemporary creatures like flukes.
And because having eye spots is better than just having light-sensing cells on your skin, it will confer an advantage to creatures who have eye spots. In an environment where creatures with eye spots compete with creatures with simple light-sensing cells, the eye-spotters will outcompete the light-sensors, and leave more offspring, and eventually drive out the competition (or force them to evolve also, of course).
And on and on, in baby steps, each step a small but noticeable improvement over the last. And it's just this sort of small, stepwise change that, over time, adds up to what we might call macro-change. At no time do any of the creatures in the progression have what we might consider a non-functional trait - they don't function nearly as well as your eyes do, to be sure, but it's not like they have half an eye. They're never sitting there with a retina and an optic nerve, just waiting in the dark for a cornea and a lens to evolve so they can finally see something.
Small changes over long periods of time are how macro-change comes about. Like I said, you're quite right to dismiss the possibility of seriously complicated traits or behaviors or anatomical structures arising in one step, since the odds would be absurdly long, and you'd most likely never see it happen in the entire history of the world. Fortunately, we all didn't have to rely on such a series of improbable events for us to come about. Certainly, as you say, the intermediate steps may be difficult to see, but it would be a rather boring universe that had its limits determined by the limits of our imaginations. ;)