cat $(find . -maxdepth 1 -name '*.png' -print | sort -V) | ffmpeg -framerate 2 -i - -vf format=yuv420p -movflags +faststart output.mp4
Many players won't like 2 fps, so if it's not working add -r 10 output option and it will duplicate frames to compensate (output will look the same, duration will be the same).
You could do a few different things:
Rename your files with padded zeroes:
Use the version sorting option:
while IFS= read -r file; do
file_args+=( -i "$file" )
done < <(ls -v *.png)
# <(ls *.png | sort -V)
The "transparent color" is the color that is mapped to transparent.
For example, if you have a web page with that image on it, and you use style sheets or absolute positioning or some other method to overlay the image on top of other items, everywhere in the gif that has that color, the items behind it (including the page's background) will show ...