Certain referenced assemblies seem to have storybrew look for the file from the app's root folder instead of the project folder.
Example given with MathNet.Numeric (after importing System.Numeric manually in Referenced Assemblies config), with Assembly Binding logging enabled:

After copy-pasting MathNet.Numeric into the root folder, the error goes away and it executes successfully.
Other Remarks
- The DLL file still needs to be inside the project folder, or else there's a missing metadata error.
- I'm not sure if every referenced assembly that isn't in storybrew's base folder (e.g. Newtonsoft.Json) does this. I'll need more libraries as examples.
I'd like to look into this, so this issue can help keep a consolidated log of information/knowledge somewhere.