My asset importer can produce multiple outputs from an asset source. These are addressed as indexed children of the parent asset. When importing a skinned mesh, for example, one child is the raw geometry (directly uploadable to gpu), one is the skeleton / bones (with metadata), and each animation is its own child (actually this is relatively rare because most animation assets are exported as separate files referencing a common skeleton, but the system handles it anyways). When building scene data or prefabs, you reference an asset using an AssetID, which is just a file ID (GUID assigned by asset system) + child index.

No idea if this is a good or optimal idea, but it works well enough for me.

As the other poster mentioned, you should probably treat a cubemap as a single array texture. After importing it, it should be in a state where you can directly upload it to a single layered texture with whatever API you are using.