It doesn't surprise me that it wouldn't work on the MACO officer's drone, but it does work on Support Drones of boffs with that ability.

As a note- there are two types of drones an engineer can possibly summon; Support Drones (innate Engineer Captain power and Rank I can be trained to boffs) and Seeker Drones (kit power).

The MACO officer's drone may be in its own category, but even if not, it would be considered a Seeker Drone. Those aren't affected by the Fabrication Engineer, anyway.