MP4Box can limit the duration of the import. You can check:
MP4Box -h import
This will show the following option:
":dur=D" imports only the first D seconds
You can use it as follows:
mp4box -add <video> -add <audio>:dur=120 <outputfile>.mp4
Note that I removed the -flat
option as you probably want to have a progressive file, with audio and video interleaving.