Thanks for the analysis. Be aware that the project isn’t finished and there are other patches that should land to get stuff better. From a developer perspective it is better to use multiple smaller patches.
As you mentioned the file output node is a known issue as the compositor (including file output node) doesn’t take meta data into account. Somehow/somewhere a mapping needs to be made from the render result meta data and the meta data that is needed when using the file output node. The mapping is needed as the layer names could be totally different. I am not sure if this re-mapping is required by other tools. This is a specific topic as Blender supports any areas of a studio pipeline and the compositor is sometimes ‘mis-used’ as a pipeline integration tool. Many of these tasks should be made accessible via BPY or as regular output settings or via a nodal pipeline editor.
Cycles and EEVEE share the same properties and the goal is to have the implementation act the same (what will be done by the patches already available). About the API there is some discussion on the actual use case Cryptomatte BPY API If you could detail your use case there we should be able to design an API that suit the needs.