AFAIK since V3.24 the padding in FLAC files is set automatically:
[2024-01-23] CHG: optimization function for FLAC files now preserves a small padding block to increase performance for possible tag modifications. (#60372)
and as @LyricsLover wrote:
[2024-01-18] NEW: added optimization function to remove padding from FLAC files to Utils submenu in right-click context menu. (#60372)
So, which version are you using?