however it is possible that the fqdn is simply a hostname

Basic debugging checklist say you should give an example, cause the way I understand it, hostname/fqdn/domain are all the same thing

Add use re 'debug'; in a short file like this to see how the engine matches the regex

for( 'hd_defect-onomatopeia', 'hd_defect-host.foo.bar.com' ){
    if( m{hd_defect-( ([^\.]+$) | (?: ([^\.]+).(.+$) ) )}sx ){
      my $fqdn = $1;
      my $host  = $2;
      defined $host or $host = $3;
      $dom = $4;
       defined $dom or $dom = $fqdn;
       print "fqdn( $fqdn) host( $host) dom( $dom )\n";
    }
}
__END__
fqdn( onomatopeia) host( onomatopeia) dom( onomatopeia )
fqdn( host.foo.bar.com) host( host) dom( foo.bar.com )
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YAPE::Regex::Explain can help to explain simple regex syntax like this

use YAPE::Regex::Explain;
print YAPE::Regex::Explain->new(
qr{hd_defect-( ([^\.]+$) | (?: ([^\.]+).(.+$) ) )}sx
)->explain;
__END__
The regular expression:

(?sx-im:hd_defect-( ([^\.]+$) | (?: ([^\.]+).(.+$) ) ))

matches as follows:

NODE                     EXPLANATION
----------------------------------------------------------------------
(?sx-im:                 group, but do not capture (with . matching
                         \n) (disregarding whitespace and comments)
                         (case-sensitive) (with ^ and $ matching
                         normally):
----------------------------------------------------------------------
  hd_defect-               'hd_defect-'
----------------------------------------------------------------------
  (                        group and capture to \1:
----------------------------------------------------------------------
    (                        group and capture to \2:
----------------------------------------------------------------------
      [^\.]+                   any character except: '\.' (1 or more
                               times (matching the most amount
                               possible))
----------------------------------------------------------------------
      $                        before an optional \n, and the end of
                               the string
----------------------------------------------------------------------
    )                        end of \2
----------------------------------------------------------------------
   |                        OR
----------------------------------------------------------------------
    (?:                      group, but do not capture:
----------------------------------------------------------------------
      (                        group and capture to \3:
----------------------------------------------------------------------
        [^\.]+                   any character except: '\.' (1 or
                                 more times (matching the most amount
                                 possible))
----------------------------------------------------------------------
      )                        end of \3
----------------------------------------------------------------------
      .                        any character
----------------------------------------------------------------------
      (                        group and capture to \4:
----------------------------------------------------------------------
        .+                       any character (1 or more times
                                 (matching the most amount possible))
----------------------------------------------------------------------
        $                        before an optional \n, and the end
                                 of the string
----------------------------------------------------------------------
      )                        end of \4
----------------------------------------------------------------------
    )                        end of grouping
----------------------------------------------------------------------
  )                        end of \1
----------------------------------------------------------------------
)                        end of grouping
----------------------------------------------------------------------
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