Using Config::Tiny, and assuming you don't actually need it to be in %ENV, but you just want to treat them as internal "environment-style" variables, and also want to accept true environment variables

#!/usr/bin/perl -l
# in reponse to https://perlmonks.org/?node_id=11105105
use warnings;
use strict;

use Config::Tiny;
my $ini_string = do { local $/; <DATA> };
$ini_string =~ s/(?<=.);.*$//gmx;       # Config::Tiny cannot handle p
+ostfix comments

my $cfg = Config::Tiny->read_string($ini_string);

#use Data::Dumper; $Data::Dumper::Indent = 1;
#print Dumper $cfg;

# the _ key holds the main-category / top-level of your .ini file;
#   if you have multiple categories, this loop will have to be modifie
+d
foreach my $key (keys %{$cfg->{_}}) {
    while( $cfg->{_}{$key} =~ /\%(.*?)\%/g ) {
        my $var = $1;
        next unless exists $cfg->{_}{$var} or exists $ENV{$var};
        #print "\$var = >>$var<<\n";
        my $repl = exists $cfg->{_}{$var} ? $cfg->{_}{$var} : $ENV{$va
+r};
        $cfg->{_}{$key} =~ s/\%$var\%/$repl/;
    }
}

#print Dumper $cfg;
print $cfg->write_string();

__DATA__
;comments
PROJECT_HOME=D:\Scripts\Projectname\ ;comments
package1=pack_test
package1_home=%PROJECT_HOME%%package1%
subtemp=%TEMP%\subdir
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On mine, that output

PROJECT_HOME=D:\Scripts\Projectname\
package1=pack_test
package1_home=D:\Scripts\Projectname\pack_test
subtemp=C:\Users\pryrt\AppData\Local\Temp\subdir
[download]

update: finished my first sentence; sorry