Apparently this was an unintentional mistake on behalf of the artist, Josh Kirby. He was given an early draft of The Colour of Magic to read as reference for his work and, when Two-Flower was called "Four Eyes" by someone as an insult, took it literally without thinking to ask.
I mean, it was a Fantasy novel written in the 1980's - one guy having 4 eyes really isn't all that remarkable, even if it were accurate.
Still, I know what you mean about Rincewind's appearance. In my mind' eye, I always think of him as he was portrayed in the video games - 30-ish years old, with a short ginger beard (and sounding a lot like Eric Idle...).
And yet when you read The Colour of Magic and The Lite Fantastic, it describes how he was in the same class as Ymper Trymon, who has spent at least a few decades working his way up through the ranks of Wizardry to become 7th Level. Depending on how long that process took, Rincewind could be anything from 30 to 60 years old!