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.
MOV is Apple's homebody: gorgeous on a Mac, awkward everywhere else. The QuickTime container; often H.264 or HEVC, sometimes heavyweight editing codecs like ProRes. That makes it the right destination when what you need is shooting and editing on Apple hardware, where it's the native tongue.