#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my $data = do{
    local $/ = undef;
    <DATA>
};


# Schlüssel
my $k = [$data =~ /#~+(\w+)~+#/sg ];

# Werte
my $v = [ $data =~ /~+#\n?(.*?)\n?#~+/sg  ];

my %cfg = ();
@cfg{@$k} = @$v;

print Dumper \%cfg; # OK

__DATA__
#~~~~~~~~~~~~~~~~foo~~~~~~~~~~~~~~~~~~~~~~~~#
bar
#~~~tempdir~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
/home/framework/files/temp
#~~~~cookiename~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
FWNG
#~~~~~mehrzeiliges~~~~~~~~~~~~~~~~~~~~~~~~~~#
Name Vorname
Am Stadtrand 123
99999 Henneberg
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#