Since you are on gentoo, can't you just build chromium with libffmpeg and then move it on a location that opera expects to find it, instead of replacing the one opera provides?
Opera looks in these locations for that "better" libffmpeg

$ cat /usr/lib/x86_64-linux-gnu/opera/resources/ffmpeg_preload_config.json [ "lib_extra/libffmpeg.so", "../../../../chromium-ffmpeg/libffmpeg.so", "/usr/lib/chromium-browser/libffmpeg.so", "/usr/lib/chromium-browser/libs/libffmpeg.so" ]