www.makemkv.com

How can I add this metaflac command to MakeMKV, so that this command will be excecuted for each FLAC file?

metaflac "File.flac" --remove-all --dont-use-padding

https://xiph.org/flac/documentation_tools_metaflac.html

MakeMKV isn't going to create FLAC files, it will create FLAC tracks within the MKV file. You would need to extract those to run them through metaflac, using something like mkvtoolnix programs.