I'm a fresh junior student doing some amo research. But my professor kept having me focus on the optics stuff. Although I learned plenty of skills, I'm also worried that this can negatively reduce my chance in applying to any real quantum optics/atomic physics labs? Since I had no real experience dealing with atoms, it might be harder to get accepted by those AMO groups? But I'm aimed to work in quantum physics.
The importance of a good understanding of optics cannot be understated in (experimental) atomic physics. I did my undergrad in condensed matter and had no difficulty getting a position in an AMO lab. What I would say is more important than direct experience with atoms is that you know your way around a lab, and I'd say your optics experience counts.