The @ISA array does not appear to work as expected.

True. I guess that's because at runtime IO::Dir::pl->new is called before its namespace is set up proper and its @ISA populated. Wrapping that namespace definition into a BEGIN block fixes that.
And you call the method read_pl(), but all you have is read() in IO::Dir::pl.

use strict;
use warnings;
use autodie; # not Autodie (update)
use IO::Dir;
my $dh = IO::Dir::pl->new('.');
while (my $file_name = $dh->read_pl()){
    print STDOUT "$file_name\n";
}

BEGIN {
    package IO::Dir::pl;
    use vars '@ISA';
    @ISA = ('IO::Dir');

    sub read_pl {
        my $self = shift;
        warn "Ok We got here.\n";
        return undef;
    }
}
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