I thought @nlents was done talking about design? Sounds like the beginning of a conversation, hopefully a better one than last time. I’m not ID, but I might take a stand at his 5 questions too.
Well, this article is a year old. It came up again on Twitter somehow, but yes, this was written partially in response to the negative things the DI had started to put out about the book (without actually reading the book, as usual). But the bigger motivation of the article was just to advertise the book to the readers of Skeptic Magazine, all or most of which are hostile to intelligent design and would see the book in that light.
I agree with you that, depending on the version of ID the proponent holds, these design quirks don’t really distinguish between purely naturalistic evolution and ID-enhanced evolution. But they are strong evidence of common descent and thus strong evidence against YEC and some of the other more fanciful versions of ID and theistic evolution. It’s interesting to me how quickly and nastily the DI came out against my book because, as you say, it’s not necessarily incompatible with their views and the book was NOT written as an argument against ID (except for side jokes here and there about the designer being incompetent, etc.). If my book is not an argument against ID, someone should tell the DI that because they certainly reacted as if it were. I suppose that might have been cleared up if they actually read the book rather than just articles about it. But, to my knowledge, none of them ever did that.