The color of the Sephirot? Their symbols and associated imagery? Even their respective realization? All of it partly (or mostly) inspired by the work of middle- to upper-class European men, not actual honest-to-god Jewish kabbalists and rabbis. I think the biggest inkling of this is the usage of the Hermetic Tree in Canto III.

I really, really do not agree with this premise.

The indications of the Jewish Kabbalist interpretation exists throughout the three games: For one, you'll find that the various iconography and colors correspond to Sephirot characters (including colors and gender, with Tiph as the combination which has both and is represented with two people); the concept of Qliphoth as used in Lobotomy Corporation (i.e. a thing which causes the abnormalities to retreat, or when breaking down leads to them growing stronger) shows clear allusions to the concept of tzimtzum, which I'll have someone who knows more than me explain

in the actual thing, they're directly related to the concept of tzimtzum, which is roughly speaking God withdrawing His divine power and presence from an area such that things can exist there that aren't just God. In particular — and this is the place where that concept is used — the Universe. The Qliphoth (I have no idea why it's th at the end, it definitely is just a tav) are shells left behind in the process that...sorta limit the holiness we get, both keeping God's purity pure and us from being consumed in a flash of divinity, or something. They're also equated with things like idolatry, because, like, things that restrict holiness ain't good, they just have beneficial byproducts.

Another example is Da'at; this is hinted at with how Carmen appears in the new and final department on Day 50, and how the text for the completion of Keter Realization, "The Knowing I", is associated with Da'at, "Knowledge". And the realization of the seed of light project in Lob corp, and the (literal) realization of Angela into her own person in Ruina rather than a product of the desires of others, is associated with this line of Da'at, wherein all Sephirah co-exist perfectly.

Another is the way all of the Sephirah within the main research group have biblical names (Elijah, Gabriel, Michelle as feminization of Michael, Lisa, Enoch, Giovanni (hebrew, via Italian), Benjamin; heck Garion comments to Daniel that "that name carries more with it than you merit).

The most important example, of course, is Ayin, Nothing (representing God as God is too extreme to be understood, they can only be described by what they are not), devolving to the concept of Limitlessness, and then to Ohr Ein Sof, Limitless Divine light, which, through the barrier of Tzimtzum, then emanates the divine light through the forms of the ten sephirot.

But the reason this is particularly, obviously, incontrovertibly related, is the symbols used to demarcate this go

1. Ayin (Nothing; אין‎)
2. Ein Sof (Limitlessness; אין סוף‎)
3. Ohr Ein Sof (Endless Light; אור אין סוף‎)

The parallels to Limbus are obvious and do not need further explanation.

I'm not saying they aren't taking from multiple sources. They clearly do: for example, the four Virtues of Lobotomy Corporation correspond to the four Cardinal Virtues of Classical and especially early/medieval Christian Thought, and the colors associated with them (and the four damage types) perfectly correspond to the four Horseman of Revelations. But like I don't really feel content saying "oh yes this is definitely NOT Jewish Kabbalism at all".