I don't know of a way to extract digital information out of a Harmony remote.
According to Yamaha documentation for the RX-V650, which is said to be electronically identical to your receiver, System Power On is NEC1 device 122, function 29, and Off is function 30.  Main Power (as opposed to Zone 2 Power) is device 126; On is function 126 and Off is function 127.

Your Atlas isn't capable of sending device 126, so you'll need to work with 122. As you've probably already found, setup code 1276 will power your receiver off. You can get a power On command by assigning a 5 digit EFC to some other button. The shift key on the Atlas remote doesn't shift the remote itself, but you can get that action by using the Setup button (top left), if you want.

First let's just demonstrate that the Atlas will power on the receiver. Do that by making sure that you've got 1276 assigned to the Audio button. Then tap Setup (don't hold it) and then enter 00248. When you press the 5th digit (8), the remote will send the On command.

Assuming that works, choose a button to assign EFC 00248 to. I think a macro button will work, and probably the two button combo <Setup> <Power>   would also work. Or any other button (like PIP On/Off) will work.

Use the 994 command (One device mode) to make the assignment. Insert a tap of Setup before step 6 if you want to use a shifted button.