Yes, it becomes completely automatic - it goes to the back of your mind and disappears, and all you think about is composition.
The comparison to driving a car is a good one. I'd take it even a step further - yes, you can drive most cars, but when you get into another car, it takes a while till you feel really comfortable again. You never drive the same way in a rental as you do your own car.
I have three cameras that are very different, and switching between them always takes me a while. We also have three cars in the family, and I always remember the basics, but in my primary car I don't have to remember which radio station is on which button, or how to adjsut the seat - I just know. That kind of unimportant stuff makes the difference between feeling really comfortable, and having to get reacquainted. Same with my cameras - I have a dRF, a dSLR, and a digital compact, and I always need a half hour to get back into the groove - but the basic knowledge is embedded for good, that stuff I don't think about anymore.
The same will happen to you.