Sorry, guys. A bit of a false alarm. I was using Brave, not true Chromium. Since the codebases are so close, I suspected it would be a Chromium issue. It seems not to be. I started up a fresh Chromium instance and it had my custom Trusted CA that are in /usr/local/share/ca-certificates.
I'll have to take a look at how Brave looks up those certificates. I have a feeling they broke something when they move the configuration directory from /etc/chromium to /etc/brave and the way that update-ca-certificates updates the system certificates.