So, this was an interesting 4 hours of reading. Thank you for the fascinating history on how colonialism and Christianity tried to steal Japanese culture and claim it as it's own. Overall, I enjoyed reading it, but I find your argument dubious and poorly made. Essentially, my counter argument is thus: Just because they're utilizing JJCAT as an occult background doesn't mean that they're anti-Semitic at all. The SMTII version of Yahweh is the Old Testament one - which you yourself assert wasn't involved with JJCAT or anti-semitic in anyway, but the SMT3 - IVA Yahweh is clearly derivative of, and quite explicitly, the New Testament version of Yahweh. The Christian-Islamic Yahweh of the Abrahamic faiths.
I'll respond to the most relevant paragraphs that I found objectionable:
"But aside from the changes to the game's (or the series', really) entire ancient backstory, the biggest retcon introduced by this quest has to do with the Kunitsu curse's approximate 100-year sealing. Since the Raidou games take place in the early 1930s, the passage of about 100 years would unleash the curse around 2030, canonically after the events of SMT1 and during the lead-up to SMT2. Surely no coincidence, this otherwise completely arbitrary number means it's intended to provide an alternate explanation for why the Kunitsu betrayed the Amatsu with YHVH in that game, as discussed prior. But as explained above, this retcon is completely unnecessary because mythology already has a built-in reason why the Kunitsu might act that way, given the chance. Additionally, read between the lines of this curse and you'll find that it exonerates the Kunitsu with an insanity defense, characterizing them as essentially good little deities who only experienced a lapse of rationality because their brethren cavorted with a foreign pantheon to gain the upper hand. Ahhhh, that good ol' Maniacs Team nationalism and xenophobia!"
This is an entirely dubious claim. Raidou is working for Yahweh and keeping the peace in Japan. He's stopping the use of and violence made by Chaos deities and even faces off against deities with Japanese motifs and backgrounds for the sake of helping Yahweh preserve Japan's safety. Sure, it follows the divide that you speak of, but he's still protecting Japanese people via taking down dangerous Japanese deities.
http://imgur.com/32qUBhi
In short, Mem Aleph is the Mother Earth principle or the primordial goddess of the Goddess movement, yet given a form that corresponds to JJCAT. Her profile also fits Kaneko's Nocturne-era comment about YHVH being the source of everything as well, if her Hebrew name in relation to the dissemination of the "ma" particle around the world is anything to go by. However, just by being Chaotic and female, she is intrinsically YHVH's inverse even as she is also, by JJCAT reckoning, his "bunrei."
This one is totally contradicted within the main plot of Strange Journey itself, the Mother Goddesses created the universe, world, and the first humans in SJ. Yahweh came after and deposed them and sealed them away. Mem Aleph is the real creator and is distinctly stated to precede Yahweh. So, you are totally wrong in this passage.
1/3