.htaccess not coppied from conf-custom/index directory

Info
Debian 9, Ispconfig 3.1.11
Details
I am trying get a htaccess template copied during the website creation. I have created the .htacces in the Directory /usr/local/ispconfig/server/conf-custom/index . This is not copied during website creation. I have dug a bit deeper and found the php code that does the copy of files from this directory in apache2_plugin.inc.php, but the part that copies the .htaccess is commented out, could anyone explain why this is and if I remove the comments will I be asking for trouble ?
I have tested and it does copy the file when I remove the comments

 

I don't know why but surely if you modify ispconfig base, make notes and remember before you update to the next version, except that I don't think it's going to make you any issues