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Most (maybe all) SBO's used the blockoff plate. Probably not the most efficient but it was how it was done from the factory. Probably the frame design would have made a "Y" pipe impossible. I believe Thornton makes some actual manifolds without the blockoff plate.
All small blocks used the same manifolds (mostly, but they changed in later years). Factory dual exhaust had the blockoff cap on the crossover port. Lower inventory and reduced manufacturing costs seems like a valid reason for not having a specific dual exhaust version.
The crossover was much easier to install prior to dropping the engine into the frame on the assembly line. Also, as I'm finding out on my 69 wagon, not having any piping on the driver's side makes it much easier to access the linkage for the three speed column shift MT along with the clutch linkage. The only cars that didn't use the crossover on SBOs were the 1977-up Toronados, since the transaxle is in the way. Even W31s used the cap on the crossover port. You can spend stupid money for the aftermarket manifolds that simply have that hole blanked off, or you can buy real headers if performance matters to you, or you can just stop losing sleep over the cap.
Thanks for the info everybody. This was just one of those "things that make you go huh" random thoughts. Now I can file this away with all the other random knowledge I've accumulated.