M4A is AAC in Apple's favorite outfit: the audio-only MP4 your iPhone speaks natively. It was born in 2003, popularized by Apple's iTunes Store, and its real weak spot is older Windows software and stubborn car stereos that expect a .mp3.
FLV is a relic of the Flash era: the format YouTube grew up on, stranded when Flash died. The Flash Video container, typically holding old H.263, VP6 or early H.264 streams. That makes it the right destination when what you need is nothing new: today it's mostly old downloads waiting to be rescued.