I have the same problem. I have a Craftsman unit with a Learn button. For several Audis and Fords, I just press the Learn button and program without any difficulty. However, my new 2019 Atlas SEL Premium will not respond to the Learn button and I don't have a remote. Any thoughts?
I had the battery operated one installed in my 2019 S and I have a Craftsman unit as well. I think you will most likely need a remote as the car button must first learn the Craftman's codes, then the opener itself need to sync the rolling code. If you have another car that is programmed to the opener, maybe try pulling it along side the Atlas's drivers side, rolling down the windows and press and hold the other car's button, in place of the remote, to see of the Atlas picks it up and the light goes green.
The way I did it was to hold 1 and 3 to clear everything, then hold the 1 button(or whichever one you want to use) till it slow blinks yellow. Then, press and hold my garage door opener remote near the mirror(would be the steering wheel for you but this is where you can try the button in your other car) till the light goes green. After it is programmed there, you need to go to your garage door opener and press the learn button and then within 30 seconds, go and press the button in the Atlas a few times till the door starts to operate.