Using that method will be pretty heavy performance wise.
I would definitely suggest you to take a deeper look into ffmeg. I believe that it is not that hard to use, and there are simple libs for ffmeg without hustle with NDK. Take a look at this library and check if there is function that you need available.
ffmpeg -i movie.mp4 -i logo.png -filter_complex overlay output.mp4
This command would be something that you are looking for.
If you still want to use something else than ffmeg I would suggest you to take a look at MediaMetadataRetriever
public Bitmap getFrameAtTime (long timeUs)
This method would be something that you could use. It gives you bitmap to draw on. But still it is going to be slow as hell. I tried do create gifs using this method, and after some time went back to ffmeg.
Hope it helps.
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