Here are some points:
- The reference is actually a preprint available from arXiv
- There is a newer version of the paper available than the one you are citing
- As far as I know, preprint papers can usually be cited just like regular papers
- Since this is a paper, you don't actually need to include the names of the universities that have created it (unlike report)
- You would not have a report number since this is not an actual report; however, if your University guidelines mandate it, my guess would be that the arXiv number should suffice: 1605.04303v4 (for the version that you are trying to cite); note that this number is already included in the citation
Here is what Zotero gives me when I cite this paper:
I would assume that some sort of reference number would be needed when citing Government reports; as long as a report is published, I am sure there will be some way you can reference that specific version (for example, Annual Report 2015, Report No. xxxx, etc.). For unpublished work, it would be harder and you might have to dig deep to see if there is any reference number. Here is a link to the University of Western Australia citation style for reports where they state "Omit Report No. if report number not available".
That link and this one also mention cases where multiple publishers are present. Perhaps something similar can be used in cases where there are multiple universities involved? See reference 1 here, for example.