Tinfoil time for me:
So someone stumbles across some new alien biology / technology, made from some strange and advanced new materials and carrying some advanced sensory organs, in deep space (the UA). It ends up in the hands of Federal scientists. In playing with it, they discover that they can "program" it. They first program a simple test - to have the object locate it's own position in space, and repeat back where it is. The scientists shuttle these modified-UA's around, in order to collect data from multiple locations, and verifying their simple program works. Science!
Later, they discover the Artefact's biology can be used to "grow" some highly advanced alloys, given proper input. Possibly very useful stuff for making spacecraft. So the Federation brings in Core Dynamics (and maybe others) to see if they can make use of it. The corporations come up with a way to expand on the initial alien biology (barnacles) and get it to grow them even better alloys (meta-alloys). The end results of this project can be found as rare engineering materials in Fed space - Proprietary Composites and Core Dynamics Composites.
As the results of these secret projects - Barnacles and Meta-Alloys - leak to the public, the Feds find more and more people are snooping around, and even stealing their "crops". To combat this, this Federation deploys defenses around their barnacle sites, and even ends up sending a Battlecruiser to protect their investment.
Back on the other side of the project, the Federation/Corporations are still tinkering with the original UA. After Jasmina Halsey turns back up, babbling about aliens, some wonder if she made contact with the race that originally made the UA's. The Federation launches an appeal for exploration data to see if they can confirm this theory, and they are able to find very compelling evidence that the aliens of Halsey's stories were in the vicinity of where the UA's were originally found, making it possible they created them. In order to try to discover this hidden race, they again modify the UA, but this time grow a new variant, intended to seek out the aliens originally responsible for it. This is the Unknown Probe.
Needs more tinfoil: What about the shell, and UA's scanning ships? Was this programmed behavior? Maybe the UA's are evolving on their own, and incorporating their new programming (morse) into their own evolution. Maybe the Feds wanted to monitor ship activity around their grow site in the Pleiades, but figured the other sites were so far away they were less at risk of being found. Maybe something else entirely.
Hypothesis to test the tinfoil: The "hidden" behavior of the Unknown Probe may have something to do with scouting out aliens that are comfortable in witchspace (that's where they got Halsey, after all) - scanning wakes, doing something in supercruise, that sort of thing.
/wild speculation