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I'm not sure why so many are rooting for Beeper. Apple's response is 100% reasonable - you have a 3rd party service that's making money by impersonating iOS devices in order to access Apple services. Apple has no way of controlling how many devices will use Beeper and if their system can maintain a good level of service, how these Beeper devices are interacting with iMessage, and whether Beeper is actually keeping iMessage metadata private or just giving lip service.
An analogy would be like Apple is throwing this awesome concert event and Beeper found out a convincing way to fake the tickets, and are actually actively promoting, registering people and profiting off of it. In any reasonable world outfits like this would be shut down immediately and rightfully so.