Because what happens when your Braintree account gets arbitrarily frozen under PayPal's risk management policies? It might be working today, but that doesn't mean the rug won't be pulled from out underneath you, and at that stage there will be real consequences for your business, i.e. frozen funds and drama. Then you've got to do the whole migration while putting out a fire.

If you wouldn't want to do business with PayPal, you probably wouldn't want to do business with Braintree if it's owned by PayPal. A different brand doesn't mean that they're not being operated by the same masters.