Why are there fresh eyes in Lord British's chest? I asked Tim Stellmach yesterday. Here's his response:
So that people would ask that very question.
To be a little less cheeky, I recall some intention to reference the psychic brain creatures holding up Killorn Keep (the eyeballs were, I think, a drop from brain creatures) and suggest some parallel or evidence of prior contact, without a very specific story about what it all might mean.
Tim was the game's co-designer with Doug Church and Paul Neurath. He built the Scintillus Academy, Killorn Keep and Britannia levels as well.