I can see why you might feel that way. I know when I first read about it I kind of felt the same way. However as mladen pointed out concerning the differences and how they are aesthetic in nature I got past it. Both the v2 and v3 function the exact same in every way and reason you most likely bought the laptop for.
The reason why I have not pushed the issue is I see what a huge vacuum Purism is trying to fill. Try to find a laptop today that is by design meant to be user serviceable is getting close to impossible. Even thinkpads have built in batteries now. I want them to succeed more than anything so that this trend of making everything have an 18 month life span can end. But I want this trend to pickup everywhere, especially in the smartphone arena.
Obviously if the switched being on the side is a big deal to you, this might not matter. I personally like them on the hinge because I can’t accidentally turn one on or off when taking it in and out of a bag.