Well, there has to be a domain name associated with a hosting account. How else do you use web hosting?
The notion of a "primary domain" is relatively new. cPanel existed a long time before addon domains and multi domain environments were so big.
However, the notion of the "primary domain" taking hold of the account's public_html folder, that's up for debate. There is a 5 year old feature request (although it is marked as planned... take that for what it's worth) that may be caught in feature request purgatory:
Main Domain to use a subfolder like addon domains
I think a better idea would be for cPanel to get away from using the public_html folder and instead use domain name based folders in the user's home directory with a public_html symlink symbolizing the "primary domain". This would allow more seamless transition of "primary domain" names if these are ever changed.
Although, I'm not exactly sure if this is at all what you are referring to, so see my first two sentences.