The DNS checkbox would be great.
 
It's a problem because it is unneeded records at times.   Here is a case where we run into issues with this and have to manually modify a servers host header.
 
Client at has a site at clientdomain.com the same site also needs to have a host header so it responds to clientdomain.servicedomain.com.   In our case it needs to run a script that can only use the servicedomain.com address.   This same script reports back to webservice.servicedomain.com and fails because the server now thinks our DNS is authoritative for servicedomain.com because HC added DNS zones into the DNS server.
 
This is not an uncommon situation now.   This particular site is part of a facebook app cluster where facebook whitelists *.servicedomain.com and all interaction with facebook has to come from that domain.   It would be the same situation if any of our customers now tried to email @servicedomain.com.   The email would be rejected since we are not  the mx for that domain.

Right now Host header is a complete solution to add  only Host Header in current domain as well as use for parking domain.
The point is it don't create dns zone file if you add Host Header using current domain name. For example
domain = yourdomain.com
Now if you want to add a host header entry i.e " Mail2 "
mail2.yourdomain.com, in this case dns zone file will not create , infact HC will only add a Cname entry in the existing domain Yourdomain.com
 
New zone file will only create if you use host header for parking a domain. For example
domain = yourdomain.com
now if you add a host header like
mail2.newdomain.com
 
Anyway after brief discussion with management we will change the implementation of Host header where it will not be use for park domain. 
then
Host Header : It will only be use to add host header in the current website (without new dns zone file )
 
Parked Domain : Its implementation will remain same.
 
If anyone has any confusion with that then please feel free to discuss.

Host header implementation has been reviewed in build11 find out detail in this link http://forum.hostingcontroller.com/tm.aspx?m=23544