It's more or less in the same universe as Kuuga, yeah. They dropped the references after the first few episodes because aligning the timelines would make things terribly convoluted, but it remains that Kuuga's story did happen prior to Agito's, and the police in Agito developed the G system as a weapon to fight the Grongi in the event they came back, after Kuuga was gone.

The Unknown aren't Grongi, though. It's kinda complicated, but they're not the same race, just to the police they're all unknown life forms.