Re: Tones and Myx. I think the key is what events are factually confirmed vs those tainted by the viewpoint character's interpretation. Myx being hungry enough to try eating someone is part of her introduction and therefore exists outside of Pip's perspective. It's a comedic scene that's resolved quickly, but might be questionable given later reveals (imo Myx will probably be the most divisive character which is not a bad thing, but means she needs to be handled more carefully). This is opposed to Pip always seeing the good side of people even when it is a terrible idea, since the player can see things that contradict her viewpoint.
Re: Meta Stuff. Yeah I expected as much, being a leftover from time crunch is understandable. Direct Fourth Wall breaks tend to be very hit and miss... they're misses imo due to being a bit "cheap" and flat. Much more interesting are unreliable narrators, forced action, etc, as I mentioned in the other comment. MBM's meta moments are the gap between knowing the right thing to do/say, and actually doing it. Clicking a wholesome goody-two-shoes dialogue prompt is vastly easier than actually saying such a thing in reality, and that's an interesting thing to explore.
Pacing is imo the most important part of VNs due to the low level of interaction. Part of why I thought MBM was better written is down to this, where sections that would usually be slow instead build dread due to the framing device. The player is baited into thinking about each new bit of text and how it fits into what they already know. Obviously don't just reuse the flashback framing device, but giving the player more than one thread to think about at one time is a good idea.
This is a big long sorry. PS birds might not be mammals but they're all amniotes, which is close enough :^).