You can bang your head against the wall, say "This is how it should work", and keep struggling with it. Or you can incorporate what Cyclone figured out, which is the way it is actually programmed for now, and where it in fact does matter whether you open the garage door from inside the car or not.
In a nutshell, what Cyclone figured out is that the car will only send a signal automatically once per time the car has been powered on.
So if you get in your car in your garage, turn it on, and open your garage door to leave, the car is not going to close the garage door for you. On the other hand, assuming it is set up properly and otherwise working, if you either open the garage door using the wall opener, or get in the car and open the garage door using the Homelink button, but do it before you have actually powered the car on, when you pull out of your garage the car very well may close the garage door for you. You will know as soon as you power the car on if it will or it won't, as if it will, you will have the Homelink screen up, with the countdown / skip option showing. If that isn't up, the car isn't going to close the garage door for you when you leave.
Do I think this needs tweaking by Tesla? Of course. But when you write above "Why would it matter..." it makes it sound like you think it shouldn't matter, and are unaware of the fact that it has been pretty conclusively determined that for now, due to the way Tesla programmed this, it just does.