FFmpeg Batch encoding error: CRF/CQP is incompatible with 2pass
2-pass is for video encoding when using an average bitrate target. When saving to MP4, default encoder is x264 whose default encoding mode is CRF where 2-pass is not applicable. The pass system also no connection with the use of filters, which is what scale and pad are.

In any case, you can carry out scaling and padding in one command.

for %%a in (*.mp4) do ( ffmpeg -i "%%a" -vf "scale=1216:684,pad=1280:720:32:0" -preset faster "output\%%~na.mp4"
)