I'm afraid that's just bad, incomplete reporting. Yes, the controlling, relevant statutes are rooted in the Emoluments clause, but they're still codified statutes that were passed by Congress and signed into law by presidents.
"Presidential pardons are for offenses against the United States. No distinction there. How to determine what is\isnt civil?
Generally, if a statute doesn't have a CRIMINAL penalty prescibed (ie incarceration), then it's not a criminal statute. Be that as it may, what you ask seems like a simple question with a simple answer, but it's not. It's actually surprisingly unsettled law and not all legal scholars agree. As of now, it's never been fully litigated and settled by the Court. However, generally, most lawyers will say that the presidential pardon authority only extends to criminal convictions. If you're interested, there are quite a few legal papers published on the subject that explore and explain it far better than I could. Here's a more recent one from Yale...
https://digitalcommons.law.yale.edu/cgi/viewcontent.cgi?article=6224&context=fss_papers
Even if Trump's pardon power did extend to this Emoluments clause statute (and I'm very confident it wouldn't), Flynn is still screwed because this statute was not cited in the Flynn pardon. This is not something that was material to his criminal 'conviction,' so it's not covered by this pardon.
"is it the "administration" aspect of it that makes it civil?
Yes. In fact, on the DoJ website on presidential pardon, it explains that the president's pardon authority doesn't extend to 'administrative decisions' (or something like that). For instance, if you've lost your medical license due to criminal conviction and you've been pardoned, that pardon does not restore your medical license.
"I read that Flynn's maximum penalty would be 30k dollars.
I'm not sure what the 'maximum penalty' would be. I thought that if you failed to obtain approval, you would forfeit your retirement benefits for the period of time you were accepting the foreign remuneration. But honestly, I signed my own retirement paperwork a decade ago, I may not remember or just missed the 'maximum penalty' part. It's possible it is as you say. I don't know for certain.
Lastly, the scope of the pardon authority came up when Manafort was pardoned. Several outlets tackled the issue, including CNN...
https://www.politico.com/news/2021/01/11/doj-paul-manafort-trump-pardon-457378
Manaforts prosecutor (that POS) Weismann argues that they anticipated a pardon and structured his plea agree to partially survive a pardon. He sounds confident, but he's very likely exaggerating. Civil penalties pursuant to criminal conviction can be forgiven by the Executive...to a point. For instance, if you forfeit your home in lieu of paying a big criminal fine and years later, that crime is pardoned, the government doesnt' owe you a refund. That's settled law. But, if give up (or they confiscate) your home and you're quickly pardoned (before the home is auctioned), you might just get the house back. It depends how quickly those assets were liquidated by the government. BUT, all those back-taxes Manafort owed, he still owes irrespective of the pardon because tax liabilities are civil liabilities, not criminal liabilities. Why? Because we all owe taxes even though we're not convicted of crimes, right?
You rock. thanx