The difference is enforcement.
By the letter of the law, every time an artist, regardless of how respected and prolific they may be, sells a drawing of a copyrighted character owned by Marvel, DC, hell even Valiant, and sells it without authorization, it is copyright infringement.
The difference is enforcement. Because convention culture, getting sketches and autographs on your comics, and things of that nature are part of the comic industry's early DNA and are still a massive part of the hobby today, comic book publishers refrain from enforcing these rules.
However, if they wanted to make an example of somebody, they could go out there, walk the convention floor and do so. They won't however, because it's bad PR, punishing your fans.
If you're asking where the line is: there is a line to be crossed and that is the copyright holder's tolerance of behavior. This C2E2 variant is an egregious flouting of Marvel's copyright. It also sets a terrible precedent where shops can begin slapping nude bodies over Spider-Gwen, putting $ in Superman's mouth, and whatever other offensive nonsense they want. I would bet money those are the conversations being had by Marvel's attorneys this week.
To the argument that "the flag and U.S.A. graphics aren't owned by Marvel", that's true. However, they are being presented together with characters owned by Marvel and Marvel's trademarks. If you ever buy a variant and it has a "trade dress" and "virgin" option, "trade dress" is literally a term lifted straight out of the trademark statute and is a protected sub-category of trademark. So, yes Marvel does have the right to enforce how their trademarks are presented through acetate on the shelf. To accept that anybody can put public domain (copyright not owned by a private party) on any trade dress they wish is to accept the position that I could take these 750 issues and put piles of dog Sh!? on the flag, Marvel's logo, Miles' head, and Clayton Crain's name. No, Marvel would not accept that. Nor should they have to.
To the argument that "Black Flag paid for these books so they own them", correct they do own the physical book. However, those ownership rights are separate and distinct from copyrights which they do not own. Owning a CD physically does not give you the right to rip the music off the CD and send it to your friends online.
There is a fundamental misunderstanding on these boards about how the copyright, trademark, and contract law framework is operating and I think everybody should refrain from trying to opine on these things. I'm going to from this point out certainly. I'm an attorney and I would refrain from providing any sort of formal legal opinion to somebody without seeing the contract first and getting a lot more information.
There are myriad things in the world happening everyday which are technical violations of copyright law. They are usually too small to enforce. Should these violations still exist in the law in today's world? Are they good policy? Those are separate questions. For the time-being this is the law of the land in effect on the day Black Flag pushed this tripe onto the market.
While there is a criminal portion of the copyright statute and the trademark statute, they are seldom used by law enforcement in the type of context we're in here. Enforcement is, for the most part, left up to the copyright and trademark holder. For Trademark, those who do not enforce the quality control of their trademark are risking being deemed to have abandoned their mark. So, there is significant incentive to enforce. This is why so many cease and desist letters are sent, because it's the cheapest form of enforcement you can perform. Because enforcement is left to private parties, it is inconsistent, but enforcement that goes to court is usually a big deal and brought to make an example and stamp out further behavior of the sort. To the arguments of fair use, parody, etc., etc., I've said it before and I'll say it again, those are affirmative defenses and questions of fact for a jury. That means, you need to go through every stage of litigation and finally get to trial before those defenses are considered and decided upon. That is more expensive than Black Flag can afford. They would settle with Marvel long before then and no settlement with Marvel would come without a covenant by Black Flag to discontinue this behavior.
There are also contract rights at play here under Black Flag and Marvel's exclusive agreement. While we do not know the specific contents of that contract, we can guess that Marvel did not waive their rights to copyright or trademark enforcement and so all three things are in play right now. Claims for breach of contract, copyright infringement, and trademark violation are all on the table right now.