MKV is the format that hoards: video, a dozen audio tracks and every subtitle, all in one box. It was born in 2002, the open-source Matroska project, and its real weak spot is playing on TVs, iPhones and editors that never learned to open the box.
M4A is AAC in Apple's favorite outfit: the audio-only MP4 your iPhone speaks natively. An MP4 container holding only audio: usually AAC, occasionally Apple's lossless ALAC. That makes it the right destination when what you need is sounding great anywhere in the Apple ecosystem.