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This is an idea for a fan theory forum post.
The basic idea is that everything we see (not just the sepia bits) reflects the point of view of the main character in that scene. For this reason it is an anti-canonical idea. It builds, I guess, on that quote from the professors, that the purpose of the comic was to show the unreliability of narrative, or something like that. The concept is that there is no absolute objective truth in the strip, everything is filtered through the characters subconscious perceptions.
Why come up with such a (deliberately controversial) theory?
Start by looking at Klaus Wulfenbach. The more we get to know him, the more sympathetic and likable he seems. But how do we explain his torturing/experimenting (with apparent enjoyment) on captive sparks? Regardless of how you explain it (he only experiments on villains, he doesn't really do it, its all for the greater good etc.), it all seems terribly out of character for him, the further we get into the story. One way to explain it is that the entire scene with Othar is seen from Othar's perspective. We have seen how much Othar doctors reality at the best of times. According to this theory, the whole 'torture/experiment' (never actually carried out) is all a result of getting the scene from Othar's point of view. In his mind it is a story of him being threatened with insane experiments by a mad scientist.
Next I noted that almost anything sinister Klaus does (threatening people, experimenting on Doctor Dim etc.) takes place when Agatha first meets him, or when she is on the Castle. She is terrified of him, and according to this theory, this colours our perceptions of Klaus in any scene which Agatha appears in. So possibly, what we see of Dr Dmitri, for instance, is really just Agatha projecting her fears onto an innocuous handyman. Notice how in the Volume One, the terrifying tyrant we meet when Agatha is present, instantly becomes a strict but fair father in the scenes where he and Gil face the clank (and Agatha is not present). Similarly vonZinzer goes from having the upper hand over Agatha, to being under her thumb fairly quickly in their relationship. The explanation: he becomes less threatening to Agatha as she gains experience and self confidence and this is what we are seeing.
The theory explains a lot of things: Zola initially so competent and ruthless, is only so when seen by herself. When Gil is in scene with her she becomes a naive innocent needing to be saved. When Agatha is in scene, Zola becomes a pathetic foil for humour - Agatha sees here only as a thwarted rival. Similarly, the unflappable Higgs (at least in most scenes he appears in) suddenly becomes terrified of Zeetha. One way of looking at it, is that those scenes in the Bar Fight, reflect Zeetha's story of this cute guy she met in a bar, who was charmingly terrified of her. Once others are in the scene Higgs goes back to unflappable. Gil for his part obviously sees himself as a tragic clown who gets no repect from anyone. Thus in scenes where he is the main character, something always goes wrong or people end up laughing at him. When Agatha appears in a scene Gil becomes a no-nonsense hero, who still needs her help to win though.
I realise its unlikely that this theory is actually true, but it does provide a good explanation of what might otherwise be anomalies.