FFmpeg : How to replace video background color with transparency? (while capturing)
GDIgrab supplies a RGB feed so the colorkey filter can work here.

Try

ffmpeg -i 1.mp4 -f gdigrab -framerate 25 -video_size 300x200 -i title="MyWindow"
-filter_complex
"[1]split[m][a];
 [a]format=yuv444p,geq='if(gt(lum(X,Y),0),255,0)',hue=s=0[al];
 [m][al]alphamerge[ovr];
 [0][ovr]overlay=(main_w-overlay_w):main_h-overlay_h[v]"
-map "[v]" -c:v libx264 -r 25 out.mp4


You may have to use a value of near 0, if 0 doesn't capture all the transparent area.