I’m also struggling between Pro and Server.
After reading this thread some time ago I tested the setup, but the results were surprisingly. For example there were only 2 results for a search term from which I knew I had even more groups in DEVONthink than DEVONagent shows as results.
So I guessed DEVONagent searches e.g. PDF Metadata and those other records just didn’t have those metadata as they were captured via Clip to DEVONthink.
I can see the power in DEVONagent searching DEVONthink databases, but it would be important to know how DEVONagent get to its results (e.g. to prepare all DEVONthink records I want DEVONagent to consider in its results).