We have sometimes seen packages from third-party repos (Atomicorp, Atomic Rocket turtle, and others) conflict with packages that cPanel either configures or depends on. Because of this, we may not be able to provide support if you use third-party repos. If a version of a package that cPanel needs is installed from your third-party repo, we will not be able to provide support for it.
cPanel is only developed to work with the packages provided by the vendor's (CentOS, Red Hat, CloudLinux) repos. To avoid any possible issues that we may not be able to support, use only their repos.
Actually configuring yum is your responsibility of the server administrator, and it may be possible to configure it to not use packages from the third-party repos that may cause conflicts. However, this would not be something that we could help you with.
