Yeah, there are minor differences inside the animal from one species to another but they are not that different to warrant changing where you aim on a deer, elk or moose.
Giving where I placed the dots on the pic I am assuming that on other than a broadside shot one would put the bullet where it needed to go whether through the shoulder, base of the neck, or what ever. Also assuming that the original question was refering to having the option of not shooting through the shoulder.
Here are three different shot angles from my signature pic blown up. Broadside, slightly quartering to, and sevearly quartering to. Given the option of not taking out the shoulder I prefer to do so but if the shot is not presented the shoulder gets the bullet.