Theme development is the same as any other system. It's very similar to a Drupal or Wordpress commerce. I am not sure I fully see what you mean.
Obviously they don't allow you to use another payment processor, why would they? They make money by having people use their payment processor. There is no benefit to them allowing people to bypass this and implement their own payment system.
The custom checkout can be a con, but it's also a pro. It allows your customers to feel at home in a native environment. Not having to deal with every ecommerce site completely different checkout system.