As silverfox3280 says you should attach the certificate to the source. Some attach it to the citation, but personally the citation image should hold a detailed image of the information not the entire certificate. But this is my standard that I've used both in the library work I do and at the Genealogy Center where I volunteer.
You said:"The repository for items you might have in your possession, is where you, or another researcher, can get the item."
This would be true IF you knew where others could find them in public collections, but if you have a copy of a newspaper article where the newspaper does not exist and you know of no archive where THIS article/issue can be found you should enter yourself as the repository. Yes you could guess that it was some where at the Library of Congress but you would not be sure and you could not complete the "Call Number" for its actual location. Some people ( myself as well) have a nice collection of self published books (by other people) and documents that are used as sources.
You said:"Using that board of health as the source already divulges the repository. There is no need to repeat it in the "repository" box. Also, common, or standard, books don't need a repository (eg Savage's New England Dictionary or The Great Migration or etc.)"
Wrong... (Maybe the dictionary would be Yes) But just because you think a book is common does not mean anyone else does. I have plenty of source books that can be found in any GOOD Norwegian Genealogy library, but newbies don't know that it is my job to tell them. As far as the "Board of Health" being the source you are mistaking, the source is the certificate and the place you found the certificate was the "Board of Health" which is placed in the Repository Record.