I find the following sentence from the rsync 3.0.7 manual page discussion of --hard-links to be unclear: [incremental recursion] does not affect the accuracy of the transfer, just its efficiency. Does that mean ... 1) The transfer will be less efficient because rsync will transfer the contents of the file, only to discover later that the transfer was unnecessary, at which point it will toss the transferred data and hard-link the file, leaving the file system an accurate duplicate of the source, or ... 2) The file contents will be accurately copied into a new file, and you will lose the space efficiency of having the hard link. I read this as (1) and was happy, but the behavior seems to be (2). Whichever the implementation does, please clarify the documentation.
I've clarified this a bit more in the latest docs (that the reading is indeed "1").