I feel like people who call dark magical girl shows a PMMM clone are partly right. Though I wouldn't call shows like Daybreak Illusion and Mahou Shoujo Site as PMMM clones, they throw too many edgy scenes and expect it to have a massive hit. What they don't realize is that PMMM was successful not because of edge but because it had good pacing and worldbuilding.
I agree; I recall coming across a post on Tumblr once complaining about how some (mostly older) fans of PMMM have a tendency to write fanfic that basically amounts to edgy, borderline torture porn, complete with gore. I saw only the first episode of Mahou Shoujo Site and from what I gathered, it feels like the show was written with those kinds of people in mind. I get what they were going for–I have a fondness for the whole character type of “person who has a lot of bad stuff happen to them yet still tries to go on,” one of my favorite characters is even Charlie Brown, who embodies that type–but the stuff that happens to Aya Asagiri in the first episode alone was ta bit too much for me.
Aya’s character in general reminded me a lot of Himei from Sailor Nothing, but the difference was that whereas Mahou Shoujo Site crammed in a lot of bad things happening to the main character in the first episode, Sailor Nothing instead spread things out, at dramatic, plot-relevant moments, and put more scenes of Himei’s friends trying to cheer her up in-between.
PMMM itself is pretty light on gore; the two moments that come to mind for me are the aftermath of Mami vs. Charlotte, and Sayaka vs. Elsa Maria; the former is edited in a way that avoids showing the messy aftermath, but it does cut to Madoka and Sayaka’s horrified reactions, which hammers home the horror, and the latter is mostly silhouetted so you don’t see exactly how messy it gets, while still showing how broken Sayaka is becoming. And you’re right; the worldbuilding was pretty good, too, particularly in how they managed to take basic Magical Girl tropes and add an extra layer of horror to it, Kyubey being the most infamous example. The pacing was also well done in how they slowly crept in the darker stuff.