Yes, removal of padding (or at least resizing it to something that makes sense) is on my internal list of things to improve for Mp3tag. Until then, you can create this workaround using metaflac.exe (you can download it from the FLAC website, look for flac-1.3.2-win.zip).
In Mp3tag, define a user-defined tool via Options → Tools, and name it, e.g., FLAC remove padding, put the path to metaflac.exe and use the parameters
--remove --block-type=PADDING --dont-use-padding "%_path%"
If you want to remove the embedded cover and the padding in one go, the parameters are
--remove --block-type=PICTURE,PADDING --dont-use-padding "%_path%"
This will also delete any cover from the file.
You can then apply the user-defined tool from the right-click context menu of the selected file in Mp3tag.