FLV is a relic of the Flash era: the format YouTube grew up on, stranded when Flash died. It was born in 2002, Macromedia (later Adobe), for Flash Player, and its real weak spot is playing anywhere at all since Flash was switched off in 2020.
MKV is the format that hoards: video, a dozen audio tracks and every subtitle, all in one box. The Matroska container: it will hold practically any codec ever made. That makes it the right destination when what you need is high-quality rips and archives with multiple audio and subtitle tracks.