AO3 does not forbid commercial links because they think fans making money from fanworks is immoral but them making money (to run the damn site) is fine.
AO3 forbids commercial links because they are making a very specific claim about the legality of fanworks, and that claim is about noncommercial fanworks.
They’re not saying that commercialized fanworks are against the law. They’re just not prepared to host them–nor defend them in court.
In case people missed it: The OTW will not honor DMCA takedown orders that are basically, “I own X work and that’s a fanfic of it, and that’s copyright infringement so make it go away.”
The OTW says, lolnope, we don’t think that’s copyright infringement. If you disagree, sue us.
The OTW says: Disney - we will not remove explicit Mandalorian fanfic. Rowling, Warner Bros - we will not remove trans Harry Potter fanfic. Gabaldon - we are not removing Outlander fanfic no matter how much you think it’s illegal or a personal violation. Yarbro, if someone puts “The Adventure of the Gentleman in Black” on AO3, you will need to actually take it to trial to (try to) get it removed; none of this C&D order followed by fans caving because they can’t afford a lawyer.
…So far, nobody has sued them. (This is, in my mind, the strongest proof we have that fanfic is not copyright infringement. In 13 years, not a single person or company has scrounged up a lawyer and filed a lawsuit against AO3/the OTW for hosting fanworks.)
But they’re not willing to put themselves on the line for commercial works. Those get considered differently in copyright law. They’re not always infringing - there’s a whole history of parody books & songs to prove that - but the OTW is not dealing with them.
The OTW does not care if fans are making money. The OTW cares if fans making money interfere with its legal defense of its archive.
If you are not a copyright lawyer, your opinion about the situation is not going to be considered.