Their problem is that stock Android doesn't allow the user to muck around with the insides of apps, and will make it harder for you to trick the PayPal app, whi

Their problem is that stock Android doesn't allow the user to muck around with the insides of apps, and will make it harder for you to trick the PayPal app, while a custom ROM gives you full control to do unfriendly things to the app like reverse-engineering, inspecting it at runtime, and messing around with its internal state. Edit to clarify: I don't say I agree with that, I believe that if they don't want you messing around inside their app, then they shouldn't ask to be on your device.