The bug

The registries.json report is missing the following registries:

• dimension
• dimension_type
• level_stem
• worldgen/*

Code analysis

Misnamed registry

While analysing the code with Mojang's mappings to find the cause of this issue, I noticed that one registry key is faultily named:
net.minecraft.core.Registry

public static final ResourceKey<Registry<Level>> DIMENSION_REGISTRY = Registry.createRegistryKey("dimension");
public static final ResourceKey<Registry<LevelStem>> LEVEL_STEM_REGISTRY = Registry.createRegistryKey("dimension");

The LEVEL_STEM_REGISTRY has the same key as DIMENSION_REGISTRY.

Cause

The reason that the listed registries aren't added to the registries.json is that the registries are never registered themselves. Their keys are registered, but the registries themselves are not.