I can see why they made it that way, especially since the still air model came out first. For still air, having a thermostat probe resting on the top of the eggs makes it easier to keep the set temp in line with the temp near the eggs. If the probe was up in the top of the lid (like on previous models), the temp would be too low down where they eggs are.
Now for circulated air, it's not as important because the temp should (emphasis on "should") be equal everywhere after a while.
I got a new incubator that also has a wire probe, but it's wrapped around the fan cage and the end hangs down approximately where the eggs are. So there's nothing for chicks to get hung up on when they start hatching.
I'm wondering if you could remove the clear plastic bit, anchor the wire somewhere on the lid, and have the very end of the probe (the measuring point) hang down level with the top of the eggs for a good temperature read.