Don't you think your Bender wants actual printed white eyes? Mine does, he asked me to split the original head part into objects.
Holes and new geometry has been created manually at polygon level, redesigning the topography, not by dirty bool operands.
There are 3 files:
2-eyeballs prepared for single extruder printing.
3-eyeballs prepared for dual extruder printing (fits perfectly with base).
If you plan to print it with single extruder and your printer is not 100% calibrated (which does?), eyeballs surely won't fit into the holes of the base, there is no tolerance space between them but they share their faces.
But Since the surface of contact is almost a perfect cylinder, you can scale down the whole part a bit keeping the proportion right. Something like 98 - 99% (1 -2 % of reduction) should work (scale factor in Cura 0.98 - 0.99).
Update: I've already printed it with success. Eyeballs printed at 98% size perfectly fits the base. On the other hand, I got much better results rotating the base and setting support for the inner sides of the cap.
I've printed a single extruder version using: .1mm layer height, support for the base and raft for both parts (it will print fine without raft).