A good rule of thumb is just to make sure that you have good water flow over all your rocks.
Don't expect premium rocks to stay that way if you put them in the on the bottom of your tank and shade them with other rock.
The article you posted has some good points to it, but how are you supposed to make caves and caverns if you do not stack your rock. I stack my rock and have very large openings for my critters to dart in and out of. My shrimp like hanging out upside down on the tops of the caves. The open areas in between the rocks create an area for water to regularly flow through. I also have hundreds of snails and hermits to help keep everything clean.
The largest rock in my system is about 10 - 12lbs. I'm tempted to chisel some of it off so it can be it's own free standing tunnel, and it will allow more water flow.
I think the author of the article you posted was just referring to you do not want to stack your rock on top of it self to make a solid rock pile where you cannot get water to flow through it. With no water flow you can get the dead spots the author was referring to.
Just my 2 cents, and hope I didn't ramble on too much...