Ruling out potential bias isn't ad-hominem fallacy IMO. Ad-hominem fallacy relates to irrelevant personal attacks. Bias is relevant- just like citing an author's history of proven fraud would not be ad-hominem fallacy, because it is relevant.

Or, at least, that's how I see it. Anyway, I think this is fundamentally different than logical arguments. The burden of proof very much rests on the paper or study or critique. Shaky credibility raises the bar of proof. Remember, in science, new papers are not de-facto gospel until proven wrong- they must be repeatedly supported by successive studies & challenges before they are accepted as truth.

Consider, for example, datasets. There is a certain amount of implicit trust in the dataset provided in some new paper. The dataset can be fudged in ways which are undetectable, and no logical argument can refute- data is not argument. Therefore until you are prepared to replicate the dataset, you are trusting the author.