sleepydoc
Team RC
If you have two holes of identical size, ... then essentially your emergency is "larger" than the siphon, since it doesn't have a partially closed gate valve on it - even though the bulkheads are the same size. As long as that emergency drain can operate under siphon without sucking air, you've got excess capacity in your emergency compared to the primary siphon...
The good news with all of this is that it's really easy to learn in a hands-on manner. IMHO, the biggest mistake you can make is to take a formulaic approach and build something you don't understand. There are LOTS of ways to run a reef tank, drain plumbing included. Building something you don't understand is risky. Instead, I think it's better to get your hands wet (literally). If you're trying to build something that can handle an emergency, simulate an emergency and see what happens. Block off your siphon with a rag and see what happens. Unplug the pump, then plug it back in 10 seconds later before the tank has drained down. Then do it again, but let the tank drain down fully this time. Then unplug the pump and plug it back in with the rag blocking the siphon, and see if the emergency can pull a full siphon from scratch. Think up any possible scenario, then test it, and adjust if you feel you don't like the result.
The restriction at the bulkhead can cause issues - one problem I had was with snails crawling down the emergency and getting stuck at the stricture. (They never seem to be able to figure out how to turn around and crawl back up!:hmm5

Another thing to consider is that people frequently have the emergency drain close to the top of the tank. If it's within an inch or two of the top of the tank, it will entrain air and the maximum flow will be reduced.
I completely agree that being blindly following a formula is not ideal. Nothing beats actual experience. The variability in thanks and setups means rote formulas will likely never work for everyone. Unfortunately, a lot of people don't totally understand the physics of how the systems work, especially when they are first starting out. A formula at least gives them a place from which to start and learn the operation. Playing around and making your setup fail is also an excellent idea. Not only will it test the setup, but it will help you learn how it works.