Portage should preserve timestamps from ${D} during merge. See an example of why it is an issue in bug #83877, and more specifically: http://bugs.gentoo.org/show_bug.cgi?id=83877#c36 Thanks in advance. Denis.
This is fixed in trunk r6739. This patch isn't very intrusive so I'll think about merge it into the 2.1.2 branch soon if it works well in testing. I've tested with the new version of quickpkg (bug 164655) and it does proper timestamp preservation.
*** Bug 163416 has been marked as a duplicate of this bug. ***
This has been released in 2.1.2.10.