As for me, a newcoomer in Shin Megoomi Tensai series, the very essence of the series is in that developers kept /core values/ of the series throughout years constantly evolving them and never remove them in the entire history of the franchise
To illustrate this, I made a very shitty picture that shows examples of true core values of the series everybody forgot.
Through this observation I can conclude, that the whole MegaTen isn't about some philosophy and occultism, but about inserting as many softcore porn as possible.
Fate/ franchise started as an eroge with justification of porn scenes in it with plot. The same thing is with Megoomi Tensai, because in majority, if not all, games, you'll definitely find some softcore porn imagery, but not in every title you'll be able to find questions about god, lucifer, lawvschaos this whole shit.
So yeah, basically atlus were a bunch of horny nerds in the beginning and still remains a bunch of horny nerds, but more popular.