Why is there both notched and un-notched valve covers, and would the notched ones provide better clearance for the very back on the passenger side?

 

The notched covers were only used on 1967-72 big blocks in A-body cars to provide clearance to the 11" brake booster (67-72) and the HVAC box (68-72). Note that the 1967 cars only used a notched cover on the driver's side since the 64-67 HVAC box is shaped differently and doesn't pose a clearance issue. Note that the notches are NOT for clearance when the valve covers are installed. They are there to facilitate removing the covers with the engine in the car for repairs without having to remove other unrelated components.