Panel 1: We find John in his workshop telling Elizabeth that the first thing that needs to be done is to decide what kind of wood to use for her birdhouse. When he asks if pine is all right with her, she says "Okay."
Panel 2: He then loses her by using what she, Elly and Mike interpret as indecipherable gibberish and what we call mathematics; this is because he says that first, we'll (which means 'he'll') measure the bottom and sides and peak the two pieces with a 45° angle to support the roof. Since all she hears is arga-barga-hooba-dooba and since she can't actually see what she's doing because John puts everything on a high table, it's not really a surprise that Liz isn't looking at what he's doing at all and simply saying "okay" to acknowledge that he was speaking. It doesn't mean that she understood a blasted thing or cared to notice what he's doing.
Panel 3: Since he picked up on that (and also since he finally noticed that she's just grabbing stuff out of the scrap bucket because at least she can see what she's actually doing), he asks her if she's paying attention to what he's trying to show her. She admits that she isn't.
Panel 4: When she tells him that this is because she's looking for stuff to build a birdhouse with, John acts as if her inattention and just grabbing things is some sort of big surprise.
Summary: Paying attention to what people are saying and understanding details are not something Liz does much because it's not something Elly does much. It's like how she thinks cooking is dumping grub into a pot and walking away until it's done. Since John has never bothered with the silly and wasteful habit of learning who the people around him actually are or how tall they are, this comes as a shock to him.