Wild.
MangaDex. These people are running an illegal operation at the end of the day regardless of how anyone feels about it. Of course they should respect the DMCA. That is how you stay out of the crosshairs.
But making uploaders tick a checkbox that says "I have permission from the copyright holders" is ridiculous. You might as well kill the website. The administration here seems extremely naive; you cannot avoid any legal repercussions by half-assedly trying to shift the responsibility to the uploader. The intent of this website from creation was clear as fucking day and you won't be shielded if Kadokawa decides to take you to pound town. This little addition literally accomplishes only two things: average people will be scared to upload anything, and if MD gets in actual trouble, they will put additional burden on any bad faith uploaders.
If you're really pessimistic, you could also read that as MD looking for a bargaining chip by handing over said uploaders in case shit goes downhill.
There is no ass covering here. The site was created for scanlations, and has hosted thousands of illegal scanlations.
You can't put the lid back on the jar. The most you can really do is just shut down the website immediately and hope they find someone else to pursue. Of course, I don't think MD is actually in that much danger, so I'm just guessing they are scared and think this does something.
MD is living on borrowed time because of this. Massive take downs are not new - requiring permission from rights holders on a piracy site is. In about a year (probably less), you can just look elsewhere for doujinshi because that is about all you will find here. It seems very unlikely that anything uploaded in the past will stay for long because there is no point in requiring permission otherwise.
As for uploads...moving to Discord is bad. Everything in Discord is logged and much of that is outside of your control. If someone comes after you, there is no middle man: you're the one looking at the legal papers. The smaller community makes it more likely that everyone in the Discord channel becomes a person of interest too. Yet as if to compound the issue, shit still tends to die easily on Discord.
There isn't a great answer for this but Discord is probably the worst solution.
edit: Oh wait, MD is dead. Admin ghosted the website for NamiComi or some shit. Check the later posts in announcements because they aren't actually making one yet.
Peace!