Actually the $num(%tracknumber%,2) in your script should already do it. In what cases exactly is this not working? Do you save files matched against MusicBrainz metadata in the right most pane, or are you saving just files in the left pane?
Maybe remove the surrounding $if, by default the track number is only added if there is an albumartist (which should be the case unless you tag a non-album track). The script will be this then:
$if2(%albumartist%,%artist%)/$if($ne(%albumartist%,),%album%/)$if($gt(%totaldiscs%,1),%discnumber%-,)$num(%tracknumber%,2) $if(%_multiartist%,%artist% - ,)%title%