FFmpeg: Convert transparency to a certain color
The quickest way is, via the overlay filter.
ffmpeg -i in.mov -filter_complex
"[0]split=2[bg][fg];[bg]drawbox=c=blue@1:replace=1:t=fill[bg];
[bg][fg]overlay=format=auto" -c:a copy new.mov
The input is split to two copies. On one, an opaque box of the desired color is drawn over the whole frame. The 2nd copy is overlaid on top. Where the pixel is transparent in the 2nd copy, the first copy shows through.
See https://ffmpeg.org/ffmpeg-utils.html#Color for color syntax. You may want to specify the correct encoders.
You'll need ffmpeg version 4.0 or newer.