Road Movie on my Mac Mini is my one stop shop for remuxing/reencoding. It does both seamlessly with presets for all the Apple devices. A remux of an 8GB 1080p MKV file with DTS audio to an MP4/MV4 with 5.1 AAC take about 2 minutes, and all the metadata is retrieved automatically, embedded subtitles can also be included in the remux. Simples.
Well worth the $20!
Well worth the $20!