So I was irritated into solving this issue yesterday. Here is what I have learned about my problem that is not in documentation.
This error seems to only be related to the admin certs. I have broken my cert chain in nearly every way while troubleshooting, and filebeat always give better errors than just "unknown certificate" if the server chains are broken. These certs were also clearly never meant to be replaced after generation, even though you'll have no problem doing so with the server certs (as long as you follow your instances.yml). After inspecting a freshly generated admin cert and comparing it to the one from my CA it's clear that there were differences.
The product itself seems very powerful and I look forward to seeing what I can do with it.