I was so sure you'd answer something along those lines. I didn't mean that it was the ONLY technique among many others, but given your apparent disdain for flashbacks I found wise to highlight that this particular technique was not used in an attempt to take the easy road but because it suited the story really well.
The thing is that all these flashbacks are more akin to short stories than flashbacks. And labelling them as nothing more than lazy infodump is inappropriate since a great deal of care has been put into making them genuinely entertaining. They don't focus only on past events, they also take their time to introduce a historical context, an atmosphere (and we're also talking about music here, let's not forget that). These flashbacks (or short stories) happen in very differents periods of time that are cleanly separated. Saying that it always negatively affects the story couldn't be more wrong; and we have to thanks the VN medium for that as it allows a synergy between text, sound and visuals. When I'm reading you, I get the feeling that resorting to flashbacks is always a sign of some kind of writing failure that VNs readers will let slide because they're uneducated peasants who have never touched a real novel in their life (even if my bookshelf is at risk of collapse) and prefer to jack off to pretty ideas that remind them of their favorite shonen. You support that claim saying that it halts the forward progress of present events, but in Fata Morgana's case, present events aren't that important. In fact I wouldn't be surprised if someone got bored in the scenes happening between the flashbacks. But as you said, there is the possibilty that flashbacks can be done right and Fata Morgana is one example of that.
Those long scenes of "nothingness" are everything except nothingness and even though developing emotional ties may be one of the reasons for the use of these flashbacks, they're also here to contribute to the setting as I previously said. I wouldn't have enjoyed Fata Morgana as much as I did without being immersed into different eras, pretty subjective you'd say but it has a great thing going for it and that's its originality. For instance, VNs and videogames (they both share the same kind of immersion, you may compare novels and visual novels when it comes to writing style but as mediums they don't have much in common when you are "experimenting" them) throwing you into a believable version of the industrial revolution are a pretty rare occurence nowadays.
And that's the something you don't find mentioned in your extract of Conjueror's review, that I don't agree with anyway (opinions!). Because plot devices to play with the reader’s expectations and emotions are definitely present and I feel like that's his main complaint here. Otherwise, he brings out the same point as solidbatman : there are pacing issues near the end that people interpret in different ways. That's all there is to it.
Fata Morgana is mainly loved for its uniqueness and even if people may have (justified) qualms with the execution it doesn't necessarily make the story a failure in that aspect.
Even though it may be a problem that the execution didn't bother EVERYONE as it should be because the factors we use to define good writing precede even the universe and are far beyond the reach of mere mortals. Any story that can't boast Flaubert's level of prose should be ridiculed after all. Seriously, I understand the fact the we can make a distinction between "good" and "bad" writing but it should never become a criteria for people other than ourselves imo. Establishing rules that are to be followed if one wants to create a "work of art" is counterproductive, this kind of proselytism is the best way to kill innovation and creativity. It's like indirectly forcing an author to do something that pleases instead of something personal and I am against that, authors are free to agree to the "good writing" conventions if they want (and to the great pleasure of the majority of people who will read them) but making an absolutely objective analysis of any kind of writing is impossible. Negative criticism affects people far too much and I believe the only individual able to judge a work is the artist himself.
Well, most people in research of writing advice want to do something that pleases anyway.