You might use XML::XSH2. It's not "another xml module", it's a wrapper around XML::LibXML which makes many things possible. For example, you can use its hash command to hash all the versions by object id, and later use its xsh:lookup function in an XPath expression to retrieve an element from the hash.

open file.xml ;
$version := hash ../id /objects/obj/version ;
ls /objects/obj[ count(refs/id)
                 and count(refs/id[xsh:lookup('version', .) = ../../ve
+rsion])
                   = count(refs/id) ];
[download]

Update: You can define the same hashing function yourself and solve your problem in the same way:

#!/usr/bin/perl
use warnings;
use strict;
use feature qw{ say };

use XML::LibXML;
use XML::LibXML::XPathContext;

{   my %hash;
    sub hash {
        my ($var, $dom, $key, $value) = @_;
        for my $node ($dom->findnodes($value)) {
            $hash{$var}{ $node->findvalue($key) } = $node;
        }
    }
    sub lookup {
        my ($var, $key) = @_;
        $hash{$var}{$key}
    }
}


my $dom = 'XML::LibXML'->load_xml(...);
my $xpc = 'XML::LibXML::XPathContext'->new($dom);

$xpc->registerFunction('lookup', \&lookup);

hash(version => $dom, '../id', '/objects/obj/version');

my @nodes = $xpc->findnodes(
    '/objects/obj[ count(refs/id)
                   and count(refs/id[lookup("version", .) = ../../vers
+ion])
                     = count(refs/id) ]');

foreach my $node (@nodes) {
    say $node->toString(1);
}
[download]

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