https://www.vintageair.com/instructions_pdf/751163.pdf
Instructions show plate to cover it. It -looks- like the original opening is going to be reasonably blocked by the evaporator unit.
My question wasn't about losing the floor vents, but not putting fresh air through the heater. I have a V8 Pontiac Firefly (Chevy Sprint) that I built that has a fan on a heater core (no fresh air to heater core, just cabin air) and it sucks for defrost.