Hi, thanks for getting back to me.
According to Reflector, System.Workflow.ComponentModel does have a direct reference to the Compiler assembly. This is with .NET 4.0 btw, sorry if I didn't make that clear.
In any case I don't want to package the workflow assemblies -- I'm only obfuscating and merging my own assemblies and leaving workflow as a regular reference.
I've manually added the Assembly element with NotAvailable=1 in the SmartAssembly project file but thought this sounded like a bug.