How to combine and optimize ffmpeg filters to avoid encoding multiple times?
The single command will be long, but here's an example for 3 inputs.

ffmpeg -i input_01.mp4 -loop 1 -t 11 -i input_01_logo.png
       -i input_02.mp4 -loop 1 -t 11 -i input_02_logo.png
       -i input_03.mp4 -loop 1 -t 11 -i input_03_logo.png
       -filter_complex
        "[0]scale=1280:720,setsar=1[0v];
         [1]fade=t=in:st=1.5:d=0.5:alpha=1,fade=t=out:st=10.5:d=0.5:alpha=1[0l];
         [2]scale=1280:720,setsar=1[1v];
         [3]fade=t=in:st=1.5:d=0.5:alpha=1,fade=t=out:st=10.5:d=0.5:alpha=1[1l];
         [4]scale=1280:720,setsar=1[2v];
         [5]fade=t=in:st=1.5:d=0.5:alpha=1,fade=t=out:st=10.5:d=0.5:alpha=1[2l];
         [0v][0l]overlay=10:10:format=auto:enable='between(t,2,11)'[0vl];
         [1v][1l]overlay=10:10:format=auto:enable='between(t,2,11)'[1vl];
         [2v][2l]overlay=10:10:format=auto:enable='between(t,2,11)'[2vl];
         [0]pan=1c,aresample=r=44100[0a];
         [2]pan=1c,aresample=r=44100[1a];
         [4]pan=1c,aresample=r=44100[2a];
         [0vl][0a][1vl][1a][2vl][2a]concat=n=2:v=1:a=1[v][a]"
        -map "[v]" -map "[a]" -pix_fmt yuv420p output.mkv


You may need single quotes in the map depending on your shell.

Use a recent version of ffmpeg, at least 4.0