I would prefer it was not that way, but I don't think we can say It's unfair, because you have to think of what would happen without such a rule. That's where it would be unfair (IMHO).
In the old days (before the rigorous controlled group rules), we could take a company and split it into two companies. Put the rank in file employees in one company, and the HCES in the other and just set up a plan for the HCEs. The controlled group rules prevent that. If you own both companies, they are ALL your employees and they must ALL be taken into account for the non-discrimination rules. If you are willing to leave out the HCEs from the plan, then you have every right to set up a plan just for one of the companies and you will never have a problem with that. It is the provision of tax favored benefits to the HCEs that requires you look at ALL your employees (defined under the controlled group/entities under common control rules).