Lavfi & filter_complex ignore codec and pixel format

[LordHDL]

Summary: When using filtergraphs, the output video will default to yuva420p instead of being based on the codec chosen. If pixel format is manually specified, it will be reflected in the stream details but not in the actual output video.
How to reproduce: Use the -c:v and -pix_fmt commands after using -lavfi or -filter_complex.

ffmpeg -loop 1 -i ~/Desktop/FP2.tiff -i ~/Desktop/fp.mov -lavfi \
"[1:v]fps=60[video]; \
 [0:v][video]overlay=50:200:shortest=1[final]" \
-map "[final]" -map 1:a -c:v ffv1 -level 3 -c:a copy ~/Desktop/filtergraph.nut

[Elon Musk]

This is because how overlay filter works and picks output pixel format by default.
There is an option to specify output pixel format for overlay filter.

[Carl Eugen Hoyos]

The format option of the overlay filter including its default is documented.