How to cutting a video and keep all format and metadata
FFmpeg only allows you to alter/override the major brand, not the minor.

Command is 

ffmpeg -i input -ss 00:00:05 -t 100 -brand mp42 -c:v copy -c:a copy output


MP4box will allow you to override both.

mp4box -brand mp42:0 file.mp4


If you want to change the handler name as well, use

mp4box -brand mp42:0 -name 2="IsoMedia File Produce by Google" file.mp4


(2 is the track index i.e. the 2nd track)