I think the solution here involves pairing plugins and asset bundles - the user needs the plugin to unpack the DLL then the asset bundle can be handled as usual. Interesting use case, but I think also closer to an edge case.

Reproduction steps:
1. Open attached project
2. Click the menu item "Test Build/Separate Bundles For Dlls"
3. Observe emitted warnings: "Unrecognized assets cannot be included in AssetBundles: {dll file}"
4. Open the "Main" scene
5. Play the scene
6. Observe that the instantiated objects have missing MonoScript references
7. In the root of the Unity project in the folder "assetbundles/assets" open the file called "testprefab.assetbundle.manifest"
8. Observe the dependency to an assetbundle that doesn't exist

Actual result: When building a prebuilt .dll on its own in an assetbundle with the BuildPipeline.BuildAssetBundles API and then loading an assetbundle with a GameObject that uses MonoBehaviours in the .dll asset that was never built will result in a Missing MonoScript.

Expected result: The BuildPipeline.BuildAssetBundles API shouldn't emit a warning when supplied with a .dll asset, but instead build a regular assetbundle with the necessary data to enable other assetbundles to reference a MonoBehaviour or ScriptableObject in a DLL at runtime.