Soul enchanter will show enchantments which encounter rate has been set to 0 for the regular enchantment table.

For example, the Tinted enchantment from charm can be disabled through its config

Charm: https://www.curseforge.com/minecraft/mc-mods/charm-reforged

It will not show up in the regular table, but as the enchantment itself is still obtainable with cheats (JEI or creative) eidolon will rightfully show it as applicable.

This also happens with enchatments added by Wall-Jump mod: https://www.curseforge.com/minecraft/mc-mods/wall-jump

This will be fixed in the next release, although really Charm and Wall-Jump should be overriding canApplyAtEnchantingTable if they uh, didn't want their enchantments to apply at an enchanting table.

Totally agree with you, that method of "hiding" enchantments looks iffy