You may have read the article, but you obviously didn't understand it. Read the third paragraph once more. Your quote refers to the previous implementation that Beeper used.
You're not routing any messages through anyone's mac mini.
Here is the source that Beeper's implementation builds on: https://github.com/JJTech0130/pypush
You can run this completely platform independent, without a Mac or IOS device. Try it yourself. DYOR and attempt to verify before you vehemently spout more misinformation.
From what I've researched, Beeper's servers are only used when you use their push-notification service as it's not possible to use Apple's own push notifications(obviously). Everything else is done locally (encryption and what not). You don't even need an Apple ID, just a phone number.
The backend code is already open source, however their app isn't, so there is a bit of trust involved. Also, the app isn't free so that sucks. There are plans to open source it though.
You can also try iMessage using the link I sent previously, all trustless and independent from Beeper.
If Beeper decides not to open-source their app, someone capable could definitely step up as once again, the underlying tech is open source.
I advise you to DYOR if you'd like to verify any suspicions, i'm not the best at explaining things.