Your HR department needs avenues to sift through referrals and comparison points. If an individual has the certificate and compares equally with a non-certificate candidate, the first individual has signaled, through the certificate, that he is interested in the field, as well as willing to invest time and resources into advancing in that field. This is the flipside of the employee signalling.
If an applicant applies without the certificate to a post which requires it, he will recognize his cover letter/interview should make a point of demonstrating competence in the area of the certificate. This is an instance of employer signalling.
If an applicant fakes having acquired the certificate and there is an easy way to determine whether or not he is faking, then HR now has an easy sieve for removing employees willing to misrepresent their skills to obtain the job. This is a step in the HR QA process.
Some employers work outside the 'work for hire' states. If they contain a certificate requirement in a job posting with enumerated skills, they can point to ineptitude in the certificate skillset as reasons for dismissal depending on the jurisdiction they're in. This is a tool in legal's toolbox.
Perhaps the certificate system is the result of the collaboration of a number of employers attempting to pool credential and training requirements for an industry, then create requirements for credentialing into legislation to control the industry pipeline of workers. This is a method of signalling to legislators or restricting competitors by indirect means.
And so on.
Additionally, your fact pattern has a small problem: expert acting as hiring managers who have knowledge of the problems with the certificate are free to adjust their screening procedure to obtain more fully vetted candidates. The only time avoiding the certificate entirely is when the signal it provides is negative.
This doesn't mean that certs are useful, merely that they might be useful to stakeholders you aren't considering.