Not silly at all! Keep asking!
Yes, "he keeps doing" (or maybe in this context "keeps on doing") means something a little different from "He is still doing ...". Firstly, it is not limited to here and now, and secondly, it has an idea of persistence, even stubbornness, when time is short or there are other things to do. "He keeps [on] going out in the evenings, even although he knows he has to study more."
The best way to think about the different meanings of "yet" is to figure out what part of speech it has, because those meanings are quite different. In your first example, it is an adverb modifying "has eaten" and it means "up until now". In your second, it is a conjunction and it means something like "however", but perhaps with bit more of a sense of contrast and apparent contradiction. Accordingly, it doesn't quite fit in your example (and also note you should probably put a comma before it). Here's another example: "She speaks fluent English, yet she didn't learn it until she was 30".