Yes that is one of the fundamental problems with the “waiting time”-type arguments. They focus on a specific outcome, as opposed any similarly complex adaptive outcome. It essentially always reduces to the Texas sharpshooter fallacy.
As I wrote in another thread, consider the difference between these two questions:
What is the probability that this specific gene G will be duplicated, and then later mutate through this specific loss of function mutation L, and that this particular other protein P will buffer against the loss?
What is the probability that some gene will be duplicated, and then later will mutate by some loss of function mutation, and that some other protein P will buffer against the loss?
My point is that for the probability argument against such scenarios to make sense, we’d have to know at least the approximate frequency with which the general case happens, as opposed to the odds of the specific. And the same goes for so-called “waiting time” problems. What is the average waiting time for the specific case, versus the average waiting time for any similarly complex case?
How often are genes duplicated? How often do duplicates suffer loss of functions mutations? How often do duplicate genes interact in buffering ways with other proteins? If we can answer these general questions we can calculate the frequency with which such events in general would be expected to occur given population size and so on. So while any one such event looks extremely unlikely, if such cases do occur in general with some appreciable frequency, the “waiting time” problem is completely misleading.