Yes, this is very annoying with etckeeper. This is also incompatible with 
read-only root.
A solution would be either migrate constantly modified files to /var (losing 
etckeeper tracking) or just avoid replacing the file when changing nothing. I 
think staying in /etc would be better to preserve tracking when modifying the 
configuration (manually or with a GUI).

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/etc/cups/printers.conf timestamp is pointlessly updated
https://bugs.launchpad.net/bugs/511297
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