Only one of the alternates matches for any particular iteration. Because you have two captures in the regex one of them must be undefined for each match. Consider the following debugging version of your regex:

use strict;

my $chr;
$chr = "this and that";
$chr =~ s/
    (?:
        (this|that)(?{print "matched lh alt: $1 "}) # Left hand altern
+ate
        |
        (\w+)(?{print "matched rh alt: $2 "})       # Right hand alter
+nate
    )
    (?{print 'def 1' if defined ($1); print 'def 2' if defined ($2); p
+rint "\n"})
    /$1\U$2/xg;
print "$chr\n";
[download]

Prints:

matched lh alt: this def 1
matched rh alt: and def 2
matched lh alt: that def 1
this AND that
[download]

Note that only one of $1 and $2 are defined for each match.