I managed to compile FFmpeg successfuly with the following:
Code
./configure
--prefix=/usr
--enable-gpl
--enable-nonfree
--enable-static
--enable-libtheora
--enable-libvorbis
--enable-omx
--enable-omx-rpi
--enable-mmal
--enable-libxcb
--enable-libfreetype
--enable-libass
--enable-gnutls
--disable-opencl
--extra-cflags="-march=armv8-a+crc -mfpu=neon-fp-armv8 -mtune=cortex-a53"
--disable-doc
--enable-rpi
--disable-ffplay
--disable-ffprobe
--extra-libs="-L/opt/vc/lib -lbcm_host -lvcos -lvchiq_arm -lmmal -lmmal_core -lmmal_util -lvcsm"
--target-os=linux
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What I was missing from my initial post is the extra libs. Once I added those, compilation and install went fine.