Yes, the more I think about this the more I like it. As suggested, you would to find them (usually at ruin sites), defeat any defensive forces and investigate each Pylon using Xenology ground units. Once sufficient Pylons have been 'researched', the rifts close down. This would be an epic task, which could be adjusted in game options to make it harder or easier. It adds a form of end game to Aurora.
Actually, would be even more interesting if the forces from the Rifts could destroy the Pylons if they find them. And I guess if this is WH40k-themed, at some point the invasion forces would need a Planet Killer