OK, after approximately 30 minutes I gave up waiting with no apparent progress. I tried resolving the target platform (/org.eclipse.cdt.target/cdt.target) manually in the Oomph created install/workspace and that didn't work either.
In my primary dev eclipse install I deleted by bundle pool (rm -rf ./.metadata/.plugins/org.eclipse.pde.core/.bundle_pool) and press "Set as Target Platform" in cdt.target and it worked fine downloading everything again.
To me this means that some of the shared bundle pooling in Oomph may be getting in the way, but of course the earlier failure may lead to a broken state that I don't yet know how to clear up. It may also be related to Mars.1 (my primary dev eclipse install that I have not upgraded yet) vs. Mars.2 (the oomph created one)
A thing to note, CDT.setup's Targlets is not based on cdt.target. The setup file has not been updated (by me and others) when changes are made to the cdt.target. Therefore it may not deliver a working target platform anyway :-(
If anyone does get it working reliably in Oomph I would be interested to hear. Unfortunately for now I have simply not taken the time to debug the Oomph issues more than above.
Jonah