Oh. Now I'm reading davideous' comment much differently. But the title of the blog post (ie "vs") makes it seem like they aren't making it open source so that the hardware is secure.
In think the "vs" in the title is saying this: they had to choose between open source (that is functional meaning you can really use the code and re-flash the device) and the secure hardware. It was a trade off of one "vs" the other, and this is their reasoning behind that trade-off.
If Yubico did this it would be very interesting to see the reaction.