Due to that pessimism, I'd expect the first ARM based Macs that are released publicly to run inferior Apple software (this is already evident with the Apple apps in the last few years). Many things will be further crippled and lobotomized with even more sandboxing restrictions, and likely no longer resemble what a "Mac app" has meant for a very long time. There have been signs of the "non-nativeness" with the Catalyst apps. Perhaps the Finder would be thrown out in favor of a Files app ported from iOS/iPadOS. What about browser rendering engines? Would third party ones be disallowed, like they are on iOS/iPadOS/tvOS? Safari on Mac has already removed support for WebExtensions last year, leaving users who have more than casual browsing requirements to switch to Firefox (or Brave or Chrome or other browsers). With battery life, thinness and lightweight laptops considered very important by Apple, there could be many things getting axed on the new ARM Macs. Perhaps, the very first ARM based Mac would actually be a new iPad with an integrated keyboard and trackpad.
The article talks about splitting the Mac line, which certainly seems to be a practical possibility. Would we then have macOS that runs on the ARM MacBook, Mac mini and iMac lines and another macOS Pro that would continue to run on the x64 Mac Pro for a much longer time? The stage is already being set to encourage developers to build iOS/iPadOS apps and have them sold as a single bundle on Mac. It's just a matter of pushing them further with the "promise" of a single build running on all platforms (thanks, Catalyst).
Just a crazy thought on emulation of x64 apps: would Apple embrace a "streaming app" emulation, similar to game streaming services where any necessary heavy lifting is done on the server side, with the local ARM processors just handling the minimal (pre-computed) rendering and I/O?