Those are OEM LED strobe holes for when the hatch is open at the side of the road, where anything mounted to the hatch (traffic advisor or primary strobes) would not be visible. That's usually a dead giveaway that the PIU was ordered with the "ready for the road" package from Ford, which was pricey, but would be essentially ready to use as a slick-top car for supervisors, or at least needing minimal upfit to add a prisoner/K-9 cage or what have you. Here's a brochure for the newer factory options:
https://www.fleet.ford.com/resources/ford/general/pdf/police-vehicles/2017 Police Interceptor Utility Lighting Packages 10-7-16.pdf
Check inside your headlights and taillights, and behind the bumper cover on the driver's side...there's a good chance that you have hideaway (HAW) strobe light solutions front & rear, as well as a siren speaker behind the bumper. It takes a bit of work to remove those all, and leaves ugly holes that let water into the headlights & taillights if not sealed properly, so it's also good to check to make sure you don't have unsealed holes. You can see what the headlight HAWs look like in mine, in the PIU photo thread, they're in the upper rear corner inside the clear headlight lens.
The gaping hole where an extended overhead console could go was probably for a camera DVR/DVD vault with screen (that's where they usually go). Sure, it could be for a light/siren controller as folks in the other thread mentioned, but Ford included a ton of wiring for the lights and sirens in the center console area and behind the cig lighter socket plate, so I strongly doubt someone would've gone through the trouble to put the controller up-top. It'd be a great place to locate a larger overhead console if you found one that looks at home there.
I
might have a headliner with less damage than yours if you're interested. I haven't decided what to do with it yet. It came out of a wreck I'm scrapping-out. It's not nice enough that it'd be worth selling as a replacement part, but I've considered cutting it into pieces to sell as patches, too.
Man, sometimes these things just wind-up with holes everywhere.
Did you remove the light from there intentionally? That's a factory-cut hole, some options put a second big dome task light there, but I think the default & all civ models tend to have a very small LED dome light with a nearly flush-fitting black housing.