it does explain why Bashir’s father was imprisoned but the Darwin station researchers were not.
Does it?
The Darwin Station researchers are human, as are their augmented subjects. Julian Bashir does not live on Earth at the time his augmentation is discovered. The Bashir family did not get this treatment done on Earth, and given the extreme lengths they went to get Julian treated, alongside Richard's documented inability to keep a job consistently, it would have been utterly insane not to move to a different world (instead of a different city on Earth, as they actually did) after they got the treatment if this would also free them from any risk of legal repercussions.
Further, Strange New Worlds explicitly refers to this as a Federation law, and the principal reason why Illyrians are not welcome in the Federation.
The idea of deliberately creating otherwise illegal augmented people purely for the purpose of making it easier to systemically identify other augmented people is so brazenly unethical, I am at a loss for further comment.