ffmpeg greenscreen transparent while using color palette
Your command is attempting to place two streams into the GIF output (the output from paletteuse and the output from chromakey), but the GIF muxer supports only a single stream. To fix this your outputs from each filter should not be orphaned. See the filtering introduction for more info.

ffmpeg -i input.mp4 -filter_complex "[0:v]chromakey=0xE700F4,split[v0][v1];[v0]palettegen[p];[v1][p]paletteuse" output.gif



For better results use the chromakey filter before creating the palette.
With the split filter you can avoid making a temporary palette file.