I’m afraid to say I don’t understand the question. Every part of an organism comes from a complex mix of metabolism, genetics, and developmental switches. New adaptations are no exception; some element of that mix has changed, and if the result helps in the right environment, that change is likely to spread.
Gould’s essay, if memory serves, was essentially cautioning against thinking every physical feature of an organism as such a change in itself. Instead, they can be side-effects of some other underlying change; an odd toe might happen not because it is useful, but because it comes from the same change as an odd thumb. It might even happen simply because it wasn’t deleterious. This is important - and yet hardly changes the underlying principle, or that many adaptations are obvious ones.
Again, if your point is that seeing the details of exactly how mutations work is subtle, I don’t see the relevance. Sure there are intricate mechanisms in play - just as when an animal eats food or poison, or fights off a disease, let alone when it develops from a cell. The general principles in each case are plain all the same.
