bpython-desktop.patch is not needed, as can be seen in: http://git.overlays.gentoo.org/gitweb/?p=proj/portage.git;a=commitdiff;h=ad24e372f5059dc1d6688e0fd01fb4fdb38f2908 The correct solution is to install a version of sys-apps/portage >=2.1.11.32 (in 2.1 branch) or >=2.2.0_alpha143.
So basically, desktop-file-validate is outputting a "hint", which older versions of portage interpret as an error. Newer versions ignore it. I suggest removing the patch without a revbump.
Dropped in 0.14