"as though he'd never seen a boy before"
This phrase is used to express that the situation of being inside someone else's house and seeing new people was completely foreign to Boo Radley. In this case, Scout's interpretation is correct in some ways, as Boo, having been stuck inside his house since he was a teenager, had not seen children, except out of his window, and on the rare occasions that he ventured outside. This represents Boo's isolation, how cut off he feels from the world, and how this affects his experiences in the outside world. Because of his isolation, Boo finds it difficult to be around other people or even be in another setting, and this discomfort is picked up on by Scout when she takes Boo to see Jem.