For whatever reason, gem rarities for me are quite literally backwards. Ancient gems are most common for me and common gems are the rarest for me. I even tried changes the configuration files and that does nothing. I am on Minecraft v1.19.2 and Apotheosis v6.0.1.

Gem rarities are not "real" in the sense that they don't actually do anything (right now)
They're based entirely on the purity (increasing at every 20% threshold value). Gem rarities will mean something in the upcoming 6.1.0 update.

Thank you for clearing the confusion.