You're telling me that when presented with two candidates, companies routinely pick the less qualified one because... The cover letter was more personalised? They put more custom messages in there? Come on. They're going to turn down a better CV for an interview because the cover letter was copy-pasted? Come on.
Companies like the best candidate they can get for the price, I honestly don't think much else matters.
For me, the presence of a cover letter with half an attempt at customisation to the company and job ad demonstrates they actually care at least a little about this role at this company. And if it's well written then that demonstrates communication skills which I value highly in my colleagues.
It's really not often clear cut which one of two CVs is the "best qualified". The cover letter is just a bit more signal that will often swing my decision towards "let's take a punt".
But why does that matter to you other than ego? Barring some exceptionally unique work your company does, we know that the applicant wants to work there because you offer money for their particular skills. Why perpetuate a culture of bullshitting?
I would then ask: if I'm a punt candidate to begin with, the number of interviews I get is primarily a factor of how many applications I fire off into the crapshoot, right? What's the increase in success rate for applications with cover letters? Is it enough to outweigh the reduction in applications I can send from hand-crafting each of them?