‘Over by’ means ‘next to’ (but yes it could also be more generally near to).

It means "by". I can't think of any example using "over by" where the word "over" serves an important purpose. All it does, as far as I can tell, is make a statement more vague, conversational, and possibly place additional emphasis on a direction of motion. "Over" in such contexts is similar to "yonder": "The apples are yonder by the front."