Consider a refrigerator with a freezer, the usual sort of thing with two compartments and two doors. It will probably not have two independent cooling systems.
Now suppose you control how much cooling you get and how much goes to which compartment. That gives you complete control, right? Except that you can spend days getting it right, particularly if it's not well labeled. There's no clear way to make the freezer colder without affecting the refrigerator temperature. All you can do is turn up the cooling and the amount going to the freezer.
That's two functions not being orthogonal, or independent.
Now suppose that you have one knob for each compartment, and it's the refrigerator's job to figure it out. It will have thermometers in each compartment, and adjust appropriately. If you want to keep the ice cream harder without freezing the milk, you adjust the freezer control.
That's two functions being orthogonal.
It should be obvious which is easier to use.