A lot of websites like these rely on legal loopholes or specific interpretations of local law in order to be left alone by governments. Kind of like AO3 and the whole concept of "transformative works".
Fanfiction is fundamentally different than manga scanlation, though. The equivalent to scanlation in this case would be taking a book, The Hobbit for example, and making an unlicensed translation rather than any kind of a fan work based on the characters or the setting. There are many who argue that fanfiction is illegal anyway, as it is using copyrighted characters and settings, but it is certainly a more grey area than just outright making a 1-on-1 translation of the original work into a different language.
I do not know of any scanlated manga site that could be said operates legally, even in some grey sense. You can have a legally scanlated manga, though, if the author gives you permission (it is the author who is the important factor here, as in Japan the authors generally keep copyright and do not relinquish it to publishers), and there are examples even on this site of such cases, but I do not know of a dedicated website that hosts solely such scanlations.
Since Dynasty has a general rule of taking down works licensed for English language release, I wondered whether this might be the case here.
This is done to encourage the purchase of legal copies, in order to support the authors (as they generally get royalties on sales - not much, mind you, but something nonetheless). And even then, this rule is not strictly enforced, you will find plenty of licensed works that are still on Dynasty, they generally stay here unless directly DMCA'ed.
It is essentially a nicety, rather than being done for any legal reasons. Whether manga is licensed in English or not is generally irrelevant in regards to the illegality of scanlation. And mind you, this is something that people should be kept aware of, as many incidents were had over western fans openly posting on social media about scanlated manga they are following, leading to DMCA's when authors discover such tweets (which is also what happened in this particular case). Be smart, people.