One point of inspiration may in fact be the Sannai-Maruyama settlement believed to have been settled some time around 3900BCE during the Jōmon period, discovered during excavation near the Okidate river in Aomori Prefecture. Though there's some resemblance to Sannai-Maruyama, even including underground storage rooms, I feel like the aesthetic of the Alph Ruins is trying to imitate something else in particular. What exactly, I'm afraid I'm just not familiar enough with archaeology to know, and my fleeting research turned up few helpful leads.

I'm going to use the original Crystal version of the inscriptions because they're honestly just better than the HGSS version, for some unknown reason. The meaning is absolutely the same between versions so it really doesn't matter they're just worded better.

𝖮𝖴𝖱 𝖶𝖮𝖱𝖣𝖲 𝖲𝖧𝖠𝖫𝖫 𝖱𝖤𝖬𝖠𝖨𝖭 𝖧𝖤𝖱𝖤 𝖥𝖮𝖱 𝖳𝖧𝖤 𝖠𝖦𝖤𝖲.
𝖳𝖧𝖴𝖲 𝖶𝖤 𝖲𝖧𝖠𝖫𝖫 𝖤𝖱𝖤𝖢𝖳 𝖠 𝖯𝖮𝖪É𝖬𝖮𝖭 𝖲𝖳𝖠𝖳𝖴𝖤 𝖮𝖴𝖳𝖲𝖨𝖣𝖤.
𝖶𝖤 𝖧𝖴𝖬𝖠𝖭𝖲 𝖬𝖴𝖲𝖳 𝖫𝖤𝖠𝖱𝖭 𝖳𝖮 𝖶𝖠𝖫𝖪 𝖨𝖭 𝖧𝖠𝖱𝖬𝖮𝖭𝖸 𝖶𝖨𝖳𝖧 𝖳𝖧𝖤𝖬. 𝖶𝖤 𝖣𝖤𝖯𝖠𝖱𝖳 𝖥𝖮𝖱 𝖳𝖧𝖤𝖨𝖱 𝖲𝖠𝖪𝖤.
𝖳𝖧𝖤𝖸 𝖯𝖮𝖲𝖲𝖤𝖲𝖲 𝖦𝖱𝖤𝖠𝖳 𝖨𝖭𝖲𝖨𝖦𝖧𝖳 𝖠𝖭𝖣 𝖱𝖤𝖥𝖴𝖲𝖤 𝖳𝖧𝖤 𝖮𝖴𝖳𝖲𝖨𝖣𝖤 𝖶𝖮𝖱𝖫𝖣.

I can't make any definitive statement as to the meaning behind this, intended or otherwise, and I don't think I'd want to. I'd much rather leave Alph up for debate, because boy howdy is there a lot to debate and a whole lot of interpretation and speculation to be done. As with all good archaeological remnants. What it does do, however, is reinforce the idea that at least part of the inspiration was taken from Japan's many Jōmon ruins, given the implication that the people who settled here did so only temporarily and ultimately migrated away at some point for whatever reason.

Yeah I'll admit this one's a lot weaker but I guess I'm just not much of an archaeologist.