MKV can hold a rich set of tracks
Matroska files may contain several audio languages, subtitles, chapters, attachments, and metadata. MP4 has different support and conventions. Decide which elements the destination needs before converting and verify the resulting track list rather than assuming the whole MKV structure was copied.
Some video and audio streams may be compatible with MP4 without re-encoding; others may require a new encode. The difference affects quality and processing. Inspect codec information when a device has specific requirements, and keep the MKV until the MP4 works in the intended player.