Here is an ebuild patch which makes synaptics install in /usr and not /usr/X11R6. See bug 90789 for the general explanation. Reproducible: Always Steps to Reproduce:
Created attachment 57531 [details, diff] synaptics-0.14.1--x11_prefix.patch
solved with synaptics-0.14.3, someone with rights please mark it "RESOLVED FIXED"
Committed.