I did not offer a "non-working solution", but a proposal, ...
which works at least for the ID3v2 tag, I have checked this before publishing, ...
what to do with it, that's your business.
Here in this thread, it was previously unknown that you want to assign empty values to tag-fields.
As you now found out, Mp3tag cannot deal with FLAC files in the wanted way, ...
when one or more empty tag-fields occur in the use of the action "Guess values".
The problem with FLAC files has been already mentioned there ...
Empty tag-field in "FLAC / Vorbis Comment" tag?
If there is displayed in the dialog "Extended Tags" one tag-field or more, having no value, ...
then a manual "Save tag" [Ctrl+S] will remove these tag-fields.
DD.20150809.0633.CEST