This is a useful analysis, though it could just as well be titled "What's wrong with biological origins theories". One can forgive the author for the title and the emphasis, given the dominance of the religious consensus that governs biological origins theory today, and thus determines what makes it through the gauntlet of "peer review" into print.
What would make the discussion more interesting is if the evolutionist proponents could see themselves, and their "just so" stories about origins, in this analysis. I'm not waiting around for that, however. There are more productive ways to invest time.
I assume you are referring to the "religious consensus" that marks the mindset of evolutionists, who, by the way, hold their theory to be unquestionably true and correct, and thus unfalsifiable.
So what is ID's theory about why there are no 600 million-year-old mammal fossils?
I agree that the author has a willful blindness towards evolution when speaking about "mini-ID". I came across this quote:
"The important scientific strategy of rendering theories testable by finding independently justified auxiliary propositions does not work for mini-ID. We have no independent evidence concerning which auxiliary propositions about the putative designers goals and abilities are true."
It could just as well be rendered:
"The important scientific strategy of rendering theories testable by finding independently justified auxiliary propositions does not work for evolution. We have no independent evidence concerning which auxiliary propositions about mutation and natural selections goals and capabilities are true."
But of course, I already agree with the ID side of things.
Not really. Evolutionary theory is thoroughly, and crucially, entwined and woven together with numerous "auxiliary" principles, as Sober calls them, which render it rich in testable implications. See, for instance, 29+ Evidences for Macroevolution.
ID by contrast is almost completely vacuous. Indeed it is intentionally vacuous. "ID proponents" systematically refuse to entertain or propose, even speculatively, any claims whatsoever about how, when, where, by what agency or in what specific forms "intelligent design" events are actually instantiated.
This intentional lack of empirical content is, I believe, due to the fact that ID is not and never was intended to function as a scientific theory. (Or a scientific program, rather. Even many IDers admit it's not sufficiently developed to qualify as a "theory".)
Instead ID's role is to serve as an inoffensive "umbrella" ideology for antievolutionists and creationists who traditionally have bitterly disagreed about numerous issues such as: the age of the earth, progressive versus sudden/fiat creationism, the "canopy" theory, the global nature (or not) of Noah's flood, the flood's geological significance, and etc, etc, etc.
In a real science, of course, such substantive disagreements would be considered fruitful. But of course creationism is concerned with putting a scientific gloss on "correct" dogma, so such disagreements are intolerable and have led to multiple schisms and/or the dissolution of antievolution orgs affected by them. (See Henry Morris' A History of Modern Creationism for many examples.)
"Intelligent Design" is, then, a "lowest common denominator" that nearly all antievolutionary creationists can support, precisely because it says almost nothing about anything.