I had to use the /closed argument. According to the official docs:
Closed
When this is set before calling Merge,
then the “transitive closure” of the
input assemblies is computed and added
to the list of input assemblies. An
assembly is considered part of the
transitive closure if it is
referenced, either directly or
indirectly, from one of the originally
specified input assemblies and it has
an external reference to one of the
input assemblies, or one of the
assemblies that has such a reference.
Complicated, but that is life…