"Are dense dark brown and black watery stool from the Colon Cleanse a sign you are getting the inner plaque out of fecal matter or is it something else?"
It depends on what you may have consumed.
Not many foods give black color of poop, unless you consumed something that is really black or something that turns black in contact with digestive juices and bile.
Blackberries and other dark berries may give black poop.
Blood can also give black color of poop, in case of bleeding that happens inside stomach, liver, bile ducts or inside small intestine.
"And do people always eventually pass calcified stones on the liver cleanse?"
No, actually, only about less than 10% of people who have their gallbladder removed surgically have calcified gallstones. Most Gallstones are made of cholesterol, at least 80% of all gallstones, which is just solidified bile. Bile is composed of bile acids, and cholesterol is composed of bile acids.
Of people who do liver flushes, very few report passing calcified stones. maybe one in 100 or one in 200.
But, many people do not catch or inspect their stones, so we do not know how often people pass calcified stones.
Also, people can pass calcified sand without even noticing it.