I built the kids some Optimist Sailboats in 1999. The boat was designed in Clearwater Fl, I got the plans from Scottland, and had help from builders in Australia and New Zealand. That's when I came to the realization that the internet had changed everything!
The hole in the first pic is where the clutch hard line attaches to the clutch flexible hose.
In the second pic, yes, the lower hole is where the OD speedo cable comes out. The tunnels were not different between the OD and non OD cars, and the hole gets covered with the seal for the handbrake later. The hole on the left was also used as an exit grommet location for the OD wiring. The early tunnels did not have a hole for the oil fill, as it had not been moved to the left side yet, and filling was through the dipstick hole. I would have to see the hole up front center. The only one that comes to mind is the battery box drain, but that is only 1/2".
You probably know the large center hole is for the shifter, and the one to the rear is access for greasing the U-joint, which is inaccessible from the bottom of the car because of the cruciform box on the frame.
So it sounds like your tunnel is normal for an early car, before the dipstick was removed from the tranny.