FFMS supports only input, LSMASH - only output.
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Err, while GPAC and LSMASH options don't conflict there maybe no need to have both enabled by default. Note, l-smash has a vapoursynth plugin (to be in ports soon) and boasts:
# /usr/local/libdata/pkgconfig/liblsmash.pc Description: Loyal to Spec of MPEG4, and Ad-hock Simple Hackwork
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FFMS=on didn't work with --disable-swscale from LAVF=off. I've split it into a separate SWSCALE option via _IMPLIES.