Hello,
First, I have done myself a type in
# 
I wanted to write "[%- END %]" should be "[%- END -%]" ... and not "[%- END %-]"
Second, "if I see some type of issues on the machine" :
as I have modified it in
/var/cpanel/templates/apache2_4/ea4_main.default
and
/var/cpanel/templates/apache2_4/ea4_main.local
to [%- END -%]
I can not say if it gives issues or not, but looking at
http://www.template-toolkit.org/docs/manual/Syntax.html#section_Outline_Tags
I see they use different combinations indeed, so it will not give problems probably :
They use
"[% END -%]" or "[%- END %]" or "[% END %]"
but never mine "[%- END -%]"
So my fault

So even if with [%- END -%] it does not give difficulties in my
/var/cpanel/templates/apache2_4/ea4_main.local
But will restore the original
/var/cpanel/templates/apache2_4/ea4_main.default
and replace the in my "[%- END -%]" with the original " [%- END %] "
/var/cpanel/templates/apache2_4/ea4_main.local
Thanks and sorry for the "false alarm" !