@Akemua Underlying tones? You probably read Rave master long ago and don't really remember the story, because the first few arcs were 100% comedy and nonsense comedy at that. Where both Haru and his enemies had ridiculously comic powers and battles ended with only the enemies becoming the butt of the joke, even the characters/countries names were stupid. Those Underlying tones of yours only came into being later, after the story was totally overhauled in later arcs, the changes were notoriously obvious and sudden at that. The amount of jokes were reduced, the clown-like enemies disappeared, the big bad stopped acting stupid, the series became another thing entirely.
I remember I was close to dropping the series back then, before the story changed like that. And only after this change did the author actually add those precious underlying tones of yours, by inserting the backstory about Sighart, enhancing Shiba's background and adding a whole tragic backstory to Elie who had no memories of her past(You can't use this as an excuse because her actual past was centuries old, as she has the looks and few past memories of only a decade, in no scene was it ever implied that she was a priestess several decades ago, much on the contrary, she was only ever shown as being a normal girl before then, a clear case of retcon in her origin story).
Also those underlying tones DOES NOT explain that last arc. During most of the series the plot and even the backstory has always shown the rave stone to be as powerful as the Dark Brings and only the Rave Masters could actually hope to face them. Gale filled that role perfectly as the main Dark Bring user, he was an extremely powerful opponent unrivaled by any other character, and only after mastering the Rave stone did Haru gain enough power to face him. In the last arc however the author retcons this fact and shows the Dark Brings as being outrageously powerful, so powerful in fact that the Rave stone only serves to allow their users to merely protect themselves and survive. Like I said, the story changed a freaking lot, and no there were no underlying tones to predic this, this time around.
The author CAN change the whole theme of the story at will and he does not need any previous setup to pull this off, as long as he properly changes the tone for the rest of the story and include other serious themes after this chapter to add enough background to it. This is possible because some stories don't really have an actual plot.
Like here, where the manga didn't really have a proper story and was just about the special cleaning of the day.
An example of this is Sket Dance, where the manga started of as pure comedy until the author decided on adding a proper story to it, and just like here he did this by the use of tragic flashback arcs to explain the reasons behind each characters personality and the reason why bosun created the Sket Dan club.
This rape flashback arc can be used to set the tone for future arcs, and just like i said dozens of times, they are exactly the same kind of thing that was used on Rave Master, and many other stories. THe only difference is that a problematic topic was used, instead of a more common tragic background. This is the author setting an "underlying tone". And yes he may have added this arc merely out of spite for getting this series cancelled, but like I said it can be used to expand his story. Most changes in setting to most series start this way. Sket Dance started off with the MC trio's background story, Rave Master, did this by adding more detail and fixing the overrall quality of the characters, Naruto did this by timeskipping and adding an actual "villains"(as in, enemies that definitely need to be defeated for some bigger purpose, as before Akatsuki we only had a random pick of local enemy bosses, or that one apprentice that had gone wrong(Orochimaru), they were random enemies that were not actually related to the big bad in any way and hed their own agendas to fufill) in a story that had none, in order to tie in with Sasuke's background.