You can apply the scale and colorkey filters before overlaying. You can then overlay multiple times, if required, in a single script. The basic concept is shown below.
ffmpeg -i background.mp4 -i mainvideo.mp4 -i greenvideo.mp4 -i logo.png -filter_complex /
[1]scale[SC];[2]colorkey[CK]; /
[0][SC]overlay[OV];[OV][CK]overlay[0][SC]overlay[OVa];[OVa][CK]overlay[OVb];[OVb][3]overlay out.mp4