From my understanding 3D secure would go a long way to help protect against chargebacks. Why not make it optional?
https://support.stripe.com/questions/does-stripe-support-3d-...
https://support.stripe.com/questions/does-stripe-support-3d-...
Essentially, they get to perform their own fraud prevention and it's a way of trying to improve confidence in online payments.
I believe the idea that it takes away rights from the customer is a misconception (I also think most of these protections are given by law).