To clarify as I think the post was a bit muddled in this description, don't think any of these are 'unorthodox magical girl shows' as the genre is largely being defind, so much as they are shows that arguably share imagery and themes with magical girl shows, and that occupy a darker space in anime. You could attempt to construct an argument that these shows have girls who are magical. Mai Hime (and especially Otome) I'd classify as straighter magical girl shows that are a bit on the darker side in a number of ways (more and less on Otome there respectively), though they have some aesthetic differences from cleaner examples.
Rather, it seems a bit easier to claim Narutaru or Elfen Lied as a predecessor to Mahou Shoujo Site in some respects than Sailor Moon, and these shows also use young women with magical powers (and cutesy aesthetics) as an excuse or backdrop for, whatever our feelings on how well it's done, darker storylines.
Here then, the point was less a strict typology, which is finnicky and hard since the classification is a bit tricky, and more to argue that it's these genre-adjacent darker shows that are more susceptible to any kind of Madoka-effect than the Pretty Cures of the world. After all, a strict genre categorization that doesn't bias against including darker shows (to show their prevalence over time, and the genre's shifting composition with time as well) would have to ignore a lot of thematic concerns.