You can reorder the chapters so that each chapter is matched with the right video.

Chapters names don't have to match videos names.

You can add multiple audios to each video file.You can set the new audio to be at the top of audios tracks in the output video.You can set audio delay, track name, language.You can set audios to be default/forced.You can reorder the audios so that each audio is matched with the right video.Audios names don't have to match videos names.You can add multiple subtitles to each video file.You can set the new subtitle to be at the top of subtitles tracks in the output video.You can set subtitle delay, track name, language.You can set subtitles to be default/forced.

You can reorder the subtitles so that each subtitle is matched with the right video.Subtitles names don't have to match videos names.

You can change default video duration/FPS.You can view media info of each file so you can keep an eye on the video tracks.App for muxing(merging) videos with with many options.

Mkvtoolnix gui how to add subtitles