The solution turns out to be so blindingly simple that I never tried it.
To get EMPTY directories installed by Install Anywhere you have to specify the directories as files in the manifest. So with the following directory structure:
- Reference <empty>
- Reference2
- testdir <empty>
- Reference3 <empty>
- Reference4 <empty>
You need to specify the entries in the manifest as F. Specifying then as D will only result in the "Reference2" directory being included.
F,$IA_PROJECT_DIR$/samples/pysys/cor_002/Reference,./samples/pysys/cor_002/Reference
F,$IA_PROJECT_DIR$/samples/pysys/cor_002/Reference2,./samples/pysys/cor_002/Reference2
F,$IA_PROJECT_DIR$/samples/pysys/cor_002/Reference3/.,./samples/pysys/cor_002/Reference3/.
F,$IA_PROJECT_DIR$/samples/pysys/cor_002/Reference4/../Reference4,./samples/pysys/cor_002/Reference4/../Reference4
Sorry to answer my own question, really wasn't the plan!