After looking at the PCBs for #Turbot Keyboard a little bit closer, taking some measurements, and then checking the gerbers and the design I realized that I have made a horrible mistake. That keyboard is almost 10% larger than intended! And then I checked the designs for Flatreus, and they have the same problem. No wonder there seemed to be so much room.
Turns out that I have recently upgraded Inkscape and it has changed the default DPI it uses to calculate units. Fritzing assumes the old DPI, so all PCB outlines I imported were bigger than designed. And then I placed all components within the outline, proportionally spaced. Of course for something like a keyboard this won't work. So I had to basically re-do the Atreus PCB from scratch.
It's more tightly packed now, of course. Also, the chip is no longer at a 45° angle, as there is no room for that. On the other hand, I re-arranged the pins a bit and added two more LEDs, for debugging and status. There is still a joystick and two tact buttons for mouse emulation.
I think this is good enough for now, so I have ordered that PCB.