Your fossil diagrams are (probably) adult creatures. The premise of the article seems to be that it's not possible to determine which of the basic five "fingers" have developed in adult birds by looking at adult skeletons.
The hoatzin adult is an interesting example of rather dramatic changes in the life cycle of the bird. Reviewing the two skeletons as fossils a few million years from now, it would be difficult to see the actual relationship.
If what the article claims is true, it would appear that the later examples of feathered dinos were a second, never completed path to feathered flight.
The later feathered dinos are often interpreted by the "sibling relationship" (birds and dinos from a common ancestor) crowd as bird descendants going back into flightlessness. The error bars in the dates are large enough that the only clear "flyer" is Archaeopteryx at about 150 million years ago.
Archaeopteryx without the feathers looks like a fairly ordinary dromaeosaur, anyway. Much of the argument is about where you draw the line between what's a dinosaur and what's a bird.
Unless the observation of vestigial fingers (the wrong ones) on early theropods is wrong. Or unless Feduccia's embrylogical study is wrong.
The trend of the evidence, at least until Feduccia's study came out, has been very much away from Feduccia's hypothesis. It's just impossible to draw the kind of line between birds and dinosaurs that should be there if the split happened as far back as he puts it.