We are hosting many web applications for our customers. As is obvious they want to use their own domains to refer to those applications, usually they want that any user tha
CNAME'ing a root record is technically not against RFC, but does have limitations meaning it is a practice that is not recommended.
Normally your root record will have multiple entries. Say, 3 for your name servers and then one for an IP address.
Per RFC:
If a CNAME RR is present at a node, no other data should be present;
And Per IETF 'Common DNS Operational and Configuration Errors' Document:
This is often attempted by inexperienced administrators as an obvious way to allow your domain name to also be a host. However, DNS servers like BIND will see the CNAME and refuse to add any other resources for that name. Since no other records are allowed to coexist with a CNAME, the NS entries are ignored. Therefore all the hosts in the podunk.xx domain are ignored as well!
References: