Oil in cooler with hoses up never (well never is a long time but it doesn't get removed) changes, it shouldn't even factor in except at initial fill. All other things being equal the oil in should = the oil out. The only variable is the size of the cooler / aftermarket oil pan that will affect initial fill up.

PS: OP, your oil will never be as clear as a complete oil change, because you're not changing ALL the oil, you're mixing in the old oil with new oil. Unless you do a couple/three complete flushes your oil will never completely change with the cooler.