Irrelevant. How often or how rarely dinosaur soft tissues are discovered doesn't tell us whether or not the author is right to conclude a close relationship between dinosaurs and chickens in this case, based on similar collagen.

Irrelevant. Though the author says there is a “mountain of evidence” that dinosaurs and birds are related, this doesn't mean there is no evidence against that claim. For all we know, there could be two equally large \"mountains\" of evidence for and against that claim. We just want to know if the similar collagen proteins found in T. Rex and chicken tissues belong in either of the two mountains: whether the collagen counts as evidence for, against, or neither.

This would be useful to evaluate the argument. If it’s highly likely for animals that aren’t closely related to share collagens, then shared collagens between dinosaurs and chickens wouldn’t necessarily indicate a close relationship, which would weaken the argument. If it’s highly unlikely, then collagens likely do signify a close relationship, which would strengthen the argument.

Irrelevant. Even if this were possible, knowing about this specific possibility wouldn't help us evaluate the broader claim that collagen works as evidence showing that dinosaurs and birds are closely related.

It doesn't matter what researchers supposed before Schweitzer's discovery. We’re interested in whether the discovery constitutes evidence that dinosaurs and birds are closely related.