How to combine and optimize ffmpeg filters to avoid encoding multiple times? I never worked with ffmpeg before and I'm wondering which optimization I can take for my situation.

In a loop I have multiple input.mp4 files which I first convert one by one to have a common scale and audio rate with this command: 

ffmpeg -i input_01.mp4 -vf 'scale=1280:720,setdar=16/9' -ar 44100 -ac 1 input_01_tmp.mp4

Later I add images to each input.mp4 files again one by one:

ffmpeg -i input_01_tmp.mp4 -i input_01_logo.png -filter_complex "[0:v][1:v]overlay=10:10:enable='between(t,2,11)',fade=t=in:start_time=1.5:d=0.5:alpha=1,fade=t=out:start_time=10.5:d=0.5:alpha=1[fg];[0][fg]overlay=format=auto,format=yuv420p" -c:a copy input_01_unified.mp4

Finally after the loop I combine them with mkvmerge:

mkvmerge -o output.mkv \+ input_01_unified.mp4 +\ input_02_unified.mp4 ...

I'm sure this is not the optimal solution and wondering how I should change it. 

Is it possible to do all of this in one command? Either for each file or for the whole process.
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