Apparent synchronization bug in rsync

I believe I have found a synchronization bug in rsync. I have a pair of 
files, which when synced with||
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|rsync --no-whole-file --inplace -S|||
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|are not| identical afterwards. All three options are required, if I 
remove any one of the the files sync correctly. I have put the two 
files, along with a minimal test script, in this GitHub repo: 
https://github.com/mark-raymond/rsync-test

This looks like a bug to me; am I missing something? If it is a bug, I'm 
happy to create an issue in GitHub.
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