I believe there might be some confusion regarding the legality of the actions mentioned in the article to which you are referring (the hush money payments and catch and kill scheme, right?). While it is true that the FEC did not prosecute or look into the matter, that does not automatically mean that the actions were legal. There are other federal and state bodies that may have jurisdiction over these matters, and in this case, it appears that the investigation has fallen under the purview of the Manhattan District Attorney's Office.
It is also important to note that the issue at hand is not solely about the hush money payments themselves, but rather the alleged falsification of business records in an attempt to conceal these payments. Falsifying records to cover up the true nature of these transactions may constitute a crime, even if the payments themselves do not.
One of the claims being made by Bragg is that the 'enhancing crime', which is the crime that enhances what would otherwise be a misdemeanor, to a felony, are the attempts by Trump and his conspirators to prevent the facts of Trump's sexual encounters with Daniels and McDougal from coming to light, and thus harming his chances in the 2016 election. Afterall, he only won by 70,000 votes in three swing states. This act can be construed as a deceptive candidacy, which is apparently illegal in NY. It won't matter, for the purpose of enhancing the misdemeanors to felonies, if the underlying crime's statute of limitations has passed, or even it if is a federal crime, and not a state crime, as I understand New York law (noting my caveat: "IANAL" these are lay opinions). Also note that in the SOF, a tax crime could also be the enhancing crime raising the misdemeanors to a felony, and that crime would fall under NY law as NY has a state income tax and NYC (and Yonkers) have a municipal tax (I believe).
Furthermore, the point about the fines paid by Clinton in relation to the Steele Dossier is not an entirely accurate comparison. The cases differ in the underlying facts, circumstances, and potential criminal charges.
As for your statement about the checks being recorded and accounted for, the concern is not just about the checks themselves, but whether they were purposefully disguised within the financial records in an effort to evade scrutiny. If it is proven that these transactions were part of a larger cover-up, then it could indeed matter, both legally and in the court of public opinion.
It is essential to consider the entire context of the case to fully understand the potential legal implications and not dismiss the investigation simply because the FEC has not pursued it.
Cheers,
Rumpole