Nearly every packaging system is able to successfully divorce building of software from offering artifacts for download let alone ops. This is arguing that having failed to design their system appropriately we ought to accept the fruits of that bad design instead of dumping Ubuntu. Compare this with apt.

Second what you describe as a defect. There being multiple sources of software is a plus it means the power is in the hands of the user to decide whom to trust. What you don't want is a situation where people must configure additional sources just to have commonly needed software. The example you provide about the Java PPA is apt, pun intended, ideally commonly required software would be provided by the vendor instead of siloed in a third party source. Of course the vendor and the license must make this possible.