I'm in a similar boat, never came across until I was doing the 'testing out to level 4' test.

No, כן is used here solely for emphasis reasons, like the 'do' in English. "Yes, I eat bread" = "כן, אני אוכל לחם".

That wouldn't include the emphasis in the sentence

Because of the כן. It works just like "do" in the English suggested translation, "I do eat bread", to express emphasis.