First it should be noted that the authors that you are refering to are secular Harvard Biologists and not the Creationist writers who summarized and excerpted the data for Creation Evolution Headlines.
Also, it's not as simple as A & B, they were comparing 7 fully mapped Genomes.
I followed the links but didn't get to the article. It wanted me to subscribe for a fee.
But I didn't really follow your logic. Given that the ancestor X had the intron, I don't see why B's retention would depend on A's retention at all. It seems to me that they would indeed be independent.
I assume they are determining what X had by looking at the introns across the 7 fully maped genomes. It would be logical to assume that if an intron is found in multiple organisms that it was inherited. Otherwise the means of acquiring the intron must be determined. Simple mutation would be ruled out since introns are strings of code involving up to 500 pairs.
To try again: given A and B have a common ancestor, and A has a feature F but B does not, we have two possibilities:
(1) acquisition by A and not by B
(2) retention by A and loss by B
If acquisition is largely random, then the probability that A acquires F is independent of what happens to B. But the converse is not true: the very fact that A has retained a feature says that it is, in some sense, 'sticky", ie likely to be retained. That's why we still have tail bones. In general, unless there is a survival penalty associated with a feature, it won't be lost.
So if A has indeed retained a feature, it is very probable that B will have retained it also. When, in violation of this expectation, we find that B lacks the feature, the correct deduction is that the "retention" hypothesis now seems less likely, and hence the acquisition hypothesis more likely.
But the above is not how the paper reasons, which is why I think it's wrong.