MP4 is the world's default video: the file that plays before anyone has to think about it. It was born in 2001, the MPEG standards group, built on Apple's QuickTime design, and its real weak spot is very little day to day: as a container its quality depends on the codec inside.
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.