Hi All,
just an update to this workaround:
Yes, you need to disable Shields (Settings > Shields > Trackers & ads blocking) to get the Enpass extension to communicate with the Enpass app. And apparently you can't whitelist the extension.
But you don't need to keep Shields disabled. As soon as the extension finds the Enpass app, you can enable Shields again. As long as you don't restart Brave and/or Enpass (or your computer), the communication appears to be working. I tested that on Windows 10 and macOS Mojave, and it worked so far.
Not exactly perfect, but at least a small silver lining
Cheers,
John