You always have to wonder with the Federation, that's why I've established that there are different camps of what the powers that be do under the table.  Garrett was into generating Metroids with both the Federation's resources and the Mocktroid research he seized from the Space Pirates.  Other parties within the Federation were interested in the X themselves...

Funnily enough, it surprises me that the Federation hasn't tried to capture Samus before now to get DNA samples to unlock Chozo relics before now.