The ebuild doesn't run python_mod_{optimize,cleanup}, leaving orphaned cruft behind on unmerge/python upgrade etc. Patch attached.
Created attachment 118501 [details, diff] pycairo-1.4.0.ebuild.diff
All pycairo versions are affected by this. Makefile itself byte-compiles .py files. The new ebuilds sed those parts from the Makefile.in out and runs python_mod_optimize/cleanup. Thanks for reporting :)