Very interesting indeed. Once upon a time, I dabbled a bit with home built PCBs using Eagle software and the photo method. I think adding a RTC is a great idea. I also like the idea of single PCB. But in lieu of that, you could also just do a simple PCB for the IR emitter and whatever other electronics you add to the project and place everything inside a project box to keep it simple and clean.
I wander if you could wire the Arduino in between the fixture's IR receiver and the fixture, allowing the remote to continue to work as well. That way you could hide the controller in a cabinet or something and still use the remote when you wanted too. And you wouldn't need the emitter.
Now I have to order one so I can monkey with it.