So to be clear my car was NOT built for the California market, it was built for Western Canada, Calgary Alberta to be exact. It also is a power disc/drum brake car.
I have attached pictures before restoration disassembly of the tunnel brake line and the clips used, and you can see both the screw/clips and the rubber plugs side by side in the pictures.
My guess regarding the screws not being put into the plug holes is because the plug holes are to large for the self tapping screws, so the holes where plugged off, and the clip/screws mounted beside them to hold the brake line. Additionally the factory clips are much different in size than the AMK reproductions as you can see they are shorter, heavier, with larger holes than the brake line dameter, and they are factory NOT replaced during the previous owner life of the car. The longer/lighter AMK style clips where originally used for the one in the tranny hump and the firewall area, but along the driveshaft hump they where short as shown in the pictures. I think the general discussion regarding this topic has evidenced that the holes where for push clips as I suspected and Jeff alluded to, and they where never used and just plugged off. Thanks for the input and discussion regarding the topic