For all future reader searching for the tool definition to remove the Cover Art and padding space for FLAC files in Ctrl+O, Tools:
Adjust the Path: to the location where you have saved the two files metaflac.exe and libFLAC.dll
if you add it in the Windows version of Mp3tag (available from here https://xiph.org/flac/download.html)
The Parameter needed to remove an existing cover and the used padding space for it:
--remove --block-type=PICTURE,PADDING --dont-use-padding "%_path%"
The explanation from the help file of metaflac for the used options:
--dont-use-padding By default metaflac tries to use padding where possible
to avoid rewriting the entire file if the metadata size
changes. Use this option to tell metaflac to not take
advantage of padding this way.
--remove
Remove one or more metadata blocks from the metadata. Unless
--dont-use-padding is specified, the blocks will be replaced with padding.