This is reasonably straightforward with Regexp::Common, though you do have to "roll-your-own" a little:

    use Regexp::Common;

    my $balanced = qr/[^()]+|$RE{balanced}{-parens=>'()'}/;

    sub extract {
        my ($want, $from) = @_;
        my $nested = qr/$balanced* \Q$want\E $balanced*/x;
        $from =~ m/( \( $nested \) | \Q$want\E )/x;
        return $1;
    }

    my $expr = '(((B,G),A,(A,B)),C,(D,(E))),F';

    for ('A'..'H') {
        print "$_: ", extract($_,$expr),"\n";
    }
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Note that I've assumed that, in the edge case where the target is unnested (e.g. 'F' in the above example), the extraction should just return target itself.

Also note the standard regexish "left-most-longest-match" behaviour when the target appears more than once (as do targets 'A' and 'B' in the example).