I've just released Mp3tag v3.23d with a new entry Utils → Optimize FLAC in the right-click context menu of FLAC files. This will remove the excess padding from the selected FLAC files.
To display existing padding, create a column with value %_tag_size_appended%. This reports the size of the padding for FLAC files, where %_tag_size_prepended% reports the size of the Vorbis Comments and embedded cover art.