ffmpeg: overlay rotated video with transparency
Breaking the process into two steps worked for me.

See my output using the commands below at http://sendvid.com/g56xjz04

The commands I used:

ffmpeg -y -i "video for overlay.mov" -vf "format=bgra, perspective=x0=0:y0=0:x1=W:y1=180, fade=in:10:1:alpha=1, fade=out:200:1:alpha=1, scale=-1:80, rotate=-0.1745:c=none:ow=rotw(-0.1745):oh=roth(-0.1745)" -c:v qtrle overlay.mov

ffmpeg -y -i "base.mov" -i "overlay.mov" -filter_complex "[0:v][1:v] overlay=100:100:eof_action=pass [v]" -map "[v]" final_out.mov


I suspect that in the single command complex filterchain, there is some bug or nuance regarding the alpha channel operations that is generating a garbled alpha channel.

If you need a single command, I think your best way forward is to submit a bug report to the ffmpeg team, including the commands and output of both the single command and two-step process.