If you move DCs out of the Domain Controllers OU, the default setup of Group Policy is not applying to the Domain Controllers anymore, as most of the important settings are applied through the "Domain Controllers" OU. See the following TechNet article that warns about this problem:
Important: Do not move any domain controller accounts out of the default Domain Controllers OU, even if some administrators log on to them to run administrative tasks. Moving these accounts will disrupt the consistent application of domain controller policies to all domains and isn't supported.
Many facilities that search for Domain Controller computer accounts search the subtree of the "Domain Controllers" OU. So placing the computer accounts in subtree may work with a lot of the software solutions out there.
However, there may be some services and applications, including analysis tools, that only search the Domain Controllers OU for DCs (by examining the GUID_DOMAIN_CONTROLLERS_CONTAINER_W value and setting a search base of "one-level"). DCs in child OUs won't be found in this case.
It is up to the owner of the solution whether they see this as a valid issue to create an update to allow accounts to be located in child OUs of "Domain Controllers".