I know it's been two weeks, but I can provide an explanation:
You have three things that you got mixed up - the legal status of the pictures used for some old SCPs (like the first SCP ever, SCP-173), the legal status of the SCP intellectual property, and the legal status of derived works.
1: some of the old SCP articles used to use copyrighted pictures, most famously 173, which was a picture of an actual, real-life sculpture ("Untitled 2004" by Izumi Kato). Some of those were permitted uses, but the wiki has since moved to open license/user provided/unowned pictures to avoid licensing trouble. As long as this manga doesn't use those original pictures there should be no problem.
2: the wiki itself is under Creative Commons, meaning that anybody can spread its contents as long as proper attribution is provided. That means that if you want to you can create any derived work (just like this manga)
3: in a way an extension of 2, is the status of those derived works. Basically, you can make anything based on SCP and sell it, but if you're just repackaging stuff (i.e. making a video recordings of SCP articles being read out loud) people are free to pirate your stuff. In case of this manga, and some other works, the degree of change from the source is so big, that they can be treated as unique, and therefore protected under copyright law.