For *.m4a files in the "Track" column, it is not possible to prefix the leading zero for track numbers 1 to 9 (01, 02, 03, ...).
Is this a question or a statement?
In any case, see also here:
It is a statement and a question at the same time.
When the data "$num(%track%,2)" is inserted when renaming the file, then the data with a zero in front is inserted into the file name: 01, 02, ..., without the need to create this new column. Although the data 01, 02, ... will be displayed in the newly created column, the data 1, 2, ... will still remain in the "Track" column.
Filename is a string so the leading zero can be manipulated and added as desired.
In the m4a format leading zeros are not permitted in this number formatted field and as such they will be dropped when saved in mp3tag.
As @MotleyG said: filenames are not tags. Tags have their rules and so have filenames. E.g. not all characters which are perfectly valid in tags are allowed in filenames.
If you want to see leading zeros regardless of the tag format, use as
Value: $num(%track%,2)
in the column definition.
Please note, that this will remove the total number of tracks, if that is part of the data.
... and aren't the leading zeros only a kludge for players that cannot sort numerically?