The codec that allows to create objects, like biomes or configured features, has two modes. Either the object is inlined or it's in a separate file and it is referenced using a resource location like minecraft:plains.
I think the inlined objects should not be allowed whatsoever, a major issue with it is when using it for biomes. This is because when inlined, these objects do not have a name, so for instance, they won't be displayed in F3 or /locatebiome . It also prevents fixing a bug like MC-202036, where the numerical id can be shifted because of datapack ordering.
The other issue (less relevant for vanilla) is that the list version can not contain both inlined and referenced objects. Which causes a lot of problems when mods try to add to the same list, (see https://github.com/MinecraftForge/MinecraftForge/pull/7582 and https://github.com/Mojang/DataFixerUpper/issues/57 ). Removing the abilitiy to inline these objects would solve that.
This is a feature (removal) request