I just updated mtr to 0.86 after it was recently stabilized and noticed the wonderful addition of filecaps for this utility. Unfortunately upon further inspection /usr/sbin/mtr is still setuid. I believe this is a bug since the ebuild clearly intends for it to use filecaps.
I'm marking this as invalid as I now believe this is a symptom rather than a bug. portage is throwing a warning claiming my system does not support filecaps when installing all new binaries in spite of the fact that I already have a numebr of filecaps binaries working. It is then setuid-ing all of the binaries rather than trusting the filecaps to work. I will be working to identify if this is a bug in fcaps.eclass or what the cause of this is.