Unlike inventory armor slots and new Smithing table GUI, Enchantment table uses the integrated texture of lapis lazuli instead separated textures of "empty_slot" series. At the same time, enchantment texture of lapis is very different from empty slot texture.
Another problem is that this texture is not removed when lapis is placed in the lapis slot, and if the lapis lazuli texture is replaced with a resource pack or a mod, it will be very conspicuous (as it was before 1.20 with Smithing table).
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We're tracking this issue in MC-259401, MC-259451, and MC-74408, so this ticket is being resolved and linked as a duplicate.
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Duplicate of MC-74408, MC-259401 and MC-259451.