No, that's not it.

I'm on 16.10 clean install and I get the warning too.
I installed:
ffmpeg (version 7:3.0.5-0ubuntu0.16.10.1)
and 
ubuntu-restricted-extras (version 65)

I don't have libavcodec-ffmpeg-extra56 I have libavcodec-extra57

Example of the warning I get:


$ ffmpeg
ffmpeg version 3.0.7-0ubuntu0.16.10.1 Copyright (c) 2000-2017 the FFmpeg developers
  built with gcc 6.2.0 (Ubuntu 6.2.0-5ubuntu12) 20161005
  configuration: --prefix=/usr --extra-version=0ubuntu0.16.10.1 --toolchain=hardened --libdir=/usr/lib/x86_64-linux-gnu --incdir=/usr/include/x86_64-linux-gnu --cc=cc --cxx=g++ --enable-gpl --enable-shared --disable-stripping --disable-decoder=libopenjpeg --disable-decoder=libschroedinger --enable-avresample --enable-avisynth --enable-gnutls --enable-ladspa --enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca --enable-libcdio --enable-libflite --enable-libfontconfig --enable-libfreetype --enable-libfribidi --enable-libgme --enable-libgsm --enable-libmodplug --enable-libmp3lame --enable-libopenjpeg --enable-libopus --enable-libpulse --enable-librubberband --enable-librtmp --enable-libschroedinger --enable-libshine --enable-libsnappy --enable-libsoxr --enable-libspeex --enable-libssh --enable-libtheora --enable-libtwolame --enable-libvorbis --enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx265 --enable-libxvid --enable-libzvbi --enable-openal --enable-opengl --enable-x11grab --enable-libdc1394 --enable-libiec61883 --enable-libzmq --enable-frei0r --enable-chromaprint --enable-libx264
  WARNING: library configuration mismatch
  avcodec     configuration: --prefix=/usr --extra-version=0ubuntu0.16.10.1 --toolchain=hardened --libdir=/usr/lib/x86_64-linux-gnu --incdir=/usr/include/x86_64-linux-gnu --cc=cc --cxx=g++ --enable-gpl --enable-shared --disable-stripping --disable-decoder=libopenjpeg --disable-decoder=libschroedinger --enable-avresample --enable-avisynth --enable-gnutls --enable-ladspa --enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca --enable-libcdio --enable-libflite --enable-libfontconfig --enable-libfreetype --enable-libfribidi --enable-libgme --enable-libgsm --enable-libmodplug --enable-libmp3lame --enable-libopenjpeg --enable-libopus --enable-libpulse --enable-librubberband --enable-librtmp --enable-libschroedinger --enable-libshine --enable-libsnappy --enable-libsoxr --enable-libspeex --enable-libssh --enable-libtheora --enable-libtwolame --enable-libvorbis --enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx265 --enable-libxvid --enable-libzvbi --enable-openal --enable-opengl --enable-x11grab --enable-libdc1394 --enable-libiec61883 --enable-libzmq --enable-frei0r --enable-chromaprint --enable-libx264 --enable-version3 --disable-doc --disable-programs --disable-avdevice --disable-avfilter --disable-avformat --disable-avresample --disable-postproc --disable-swscale --enable-libopencore_amrnb --enable-libopencore_amrwb --enable-libvo_amrwbenc
  libavutil      55. 17.103 / 55. 17.103
  libavcodec     57. 24.102 / 57. 24.102
  libavformat    57. 25.100 / 57. 25.100
  libavdevice    57.  0.101 / 57.  0.101
  libavfilter     6. 31.100 /  6. 31.100
  libavresample   3.  0.  0 /  3.  0.  0
  libswscale      4.  0.100 /  4.  0.100
  libswresample   2.  0.101 /  2.  0.101
  libpostproc    54.  0.100 / 54.  0.100
Hyper fast Audio and Video encoder
usage: ffmpeg [options] [[infile options] -i infile]... {[outfile options] outfile}...