> What do you mean by "querying the top level .com servers directly"? How are you doing that?

First, ask the root servers for the authoritative servers for the TLD you are interested in:

    $ dig @f.root-servers.net www.google.com
    
    [...]
    ;; WARNING: recursion requested but not available
    
    ;; QUESTION SECTION:
    ;www.google.com.                        IN      A
    
    ;; AUTHORITY SECTION:
    com.                    172800  IN      NS      a.gtld-servers.net.
    com.                    172800  IN      NS      b.gtld-servers.net.
    [...]
    com.                    172800  IN      NS      m.gtld-servers.net.
    
    ;; ADDITIONAL SECTION:
    a.gtld-servers.net.     172800  IN      A       192.5.6.30
    b.gtld-servers.net.     172800  IN      A       192.33.14.30
    [...]
    m.gtld-servers.net.     172800  IN      A       192.55.83.30
    a.gtld-servers.net.     172800  IN      AAAA    2001:503:a83e::2:30
    
    [...]

The root servers don't know about google.com, but suggest you ask [a-m].gtld-servers.net, which are authoritative for .com. (Other TLDs have other authoritative servers.) So let's ask l.gtld-servers.net:

    $ dig @l.gtld-servers.net www.google.com
    
    [...]
    ;; WARNING: recursion requested but not available
    
    ;; QUESTION SECTION:
    ;www.google.com.                        IN      A

    ;; AUTHORITY SECTION:
    google.com.             172800  IN      NS      ns2.google.com.
    google.com.             172800  IN      NS      ns1.google.com.
    google.com.             172800  IN      NS      ns3.google.com.
    google.com.             172800  IN      NS      ns4.google.com.
    
    ;; ADDITIONAL SECTION:
    ns2.google.com.         172800  IN      A       216.239.34.10
    [...]
    ns4.google.com.         172800  IN      A       216.239.38.10
    
    [...]

The above is an example of a registered domain ("I don't know about www.google.com, ask ns[1-4].google.com"); if the domain is not registered, it looks like this:

    $ dig @l.gtld-servers.net no-such-domain.com
    
    [...]
    ;; WARNING: recursion requested but not available
    
    ;; QUESTION SECTION:
    ;no-such-domain.com.            IN      A
    
    ;; AUTHORITY SECTION:
    com.                    900     IN      SOA     a.gtld-servers.net. nstld.verisign-grs.com. 1301905185 1800 900 604800 86400
    
    [...]

Of course, [a-m].gtld-servers.net are run by Verisign, who could use this information for front-running. I'd be very surprised if they did, though. (DNSSEC may make it possible to query for the existence of a name without revealing it to the answering server, but I'm not sure - I'd have to read up on the protocol.)