Sure. This is only my opinion so keep that in mind and its not really complete. Ill try and keep it short as well.
To get straight to the point, Yaldabaoth is actually the metaverse representation of Japans culture. There a couple of reasons for this. One is the fact that things that are created and exist in the metaverse are born from the perceptions that people in the real world. This is presented to us throughout the game right from the beginning and all the way to the end. Two, almost everything in the metaverse is based off the perception of something real. At the bottom of Mementos, you see everyone in jail cells and are inside them willingly because they felt safe within those confines. So what is something that every human would view the same and feel safe about unless they were an outsider like the Thieves? Well, it would be rules, structures, guidelines for conduct and the like that belong to a group. That is what a culture is; the rules and structures that a group of people follow. Lastly, Yaldabaoth say it was born from the peoples feelings towards order, stability, etc. As those feelings are directed towards the rules and structures of their society, it can be said that Yaldabaoth is culture given sentience.
How the game critiques Japanese culture becomes more readily noticeable once that understanding is established. Its specifically along the dimensions that gave Yaldabaoth life: order, stability, authority, etc. When you look at the various stories in the game for the characters and confidants/co-ops, its usually along these lines that they highlight the issues with Japan. Ann, Ryuji, and the MC all have stories related to either being an outsider or disturbing the established order. Yusuke, Makoto, and Haru have stories about how their deferral to an authority blinded them or restricted them. Many of the other stories have those threads but also deal with problems specific to Japan as well. Theres a lot to discuss on an individual character basis Id need to spend more time formulating and writing it, lol.
I will say that I think Akechis position in the story is particularly interesting and hes not meant to be a hidden villain at all. Hes actually meant to be a visible counterpoint to the Thieves and to be a criticism of people that have a view of what is just but avert their eyes in in lieu of maintain the status quo.
Anyway, there are a bunch of other things as well like the reason for the religious imagery and the like that help to bolster this stuff but my understanding is a bit lacking on that part so it's not terribly complete.