This is probably going to be considered useless trivia from someone who was around back then, but...bnickel said:
The rear portion of many intakes from the 70s were milled down under the secondarys like you describe, but not for any reason you would think. It is sorta neat to think that this is some sort of 'old school' trick that has been lost to time and we are rediscovering it... not so.
The reason that those notches were there was because Holley tinkered with and tried to market a 3 barrel carb during that era. It was supposed to replace 4 barrels... obviously it never did. The 3 barrel carb and the secondary notches faded away with time.
The secondarys on the 3 barrel, or secondary, was one single oval throttle plate, instead of 2 separate plates. The oval plate would swing open and need the notch in the plenum divider to operate. If there was no notch, the 3rd barrel could not open.
Externally the 3 barrel looked like any other 4150/60 Holley, the only difference was the back 2 barrels were fused together as one long oval.
My .02
Dave
Edit: More useless trivia... Holley and GM were so close during this period, ie. 780 vacuum was designed specifically for Chevy use at first, that GM put notches in a couple of it's hipo intakes from the factory. They anticipated either customers using the new wave 3v carb or maybe even going to it right from the factory in short order. Then emissions, insurance, and fuel shortages did what they did in the early 70s, destroying all those plans.