How about turning the arrays into strings and then using boolean & on them, using tr to count the 1s?
my @x = qw( 0 0 0 0 1 1 0 0 0 0 1 0 );
my @y = qw( 1 0 0 0 1 0 1 0 1 0 1 0 );
my $x = join '', @x;
my $y = join '', @y;
my $compare = $x & $y;
my $joint = $compare =~ tr/1/1/;
print "$joint\n";
Can you throw this into your benchmarking? @x obviously would need to be turned into a string only once.
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