proměnnou remove_border_alef
var remove_border_alef = $('#remove_alef').prop('checked');
nepoužíváte, máte tam natvrdo true
var transText = transliterate(hebText, { 'isSeqeunced': true, 'qametsQatan': qametsQatan, 'lang': lang, 'uppercase_tet': uppercase_tet, 'remove_border_alef': true,'uppercase': uppercase, 'comments': comments, 'alphanum': alphanum });
zkuste změnit na
var transText = transliterate(hebText, { 'isSeqeunced': true, 'qametsQatan': qametsQatan, 'lang': lang, 'uppercase_tet': uppercase_tet, 'remove_border_alef': remove_border_alef,'uppercase': uppercase, 'comments': comments, 'alphanum': alphanum });