Halide developer here. Since we're in the middle of a launch, I don't have time to dig super detailed into that article you posted, but from a quick skim it doesn't appear to be particularly well-researched.
All the goodness of the first party camera's deep fusion, etc, is exposed to third-party developers. So if you're using a third party app (that knows what they're doing) then at worst you get the same results as the first party camera.
Here are some things off the top of my head that you don't get with the first party camera, excluding RAW:
Manual focus, Control over ISO vs duration, Manual white balance, Explicit control over which lens is being used (the first party camera switches without telling you), tell what parts are clipping or hitting your noise floor (histogram, waveform, and zebras), focus loupe and focus peaking that tell you exactly what is in focus (rather than tapping and hoping for the best) a reviewer lets you view the component images that make up the image asset in your library (e.g. depth data on portrait photos)…
With MKII, we're now investing in education to help beginning photographers become better.
That said, writing this out are just the checkboxes on a spreadsheet of features. It's harder to quantify the value of design. While we think the first party camera is great, it's also tasked with doing many, many things, from videos to panoramas.
Halide is designed to only shoot photos. Not even video, just photos. We're aiming to be the absolute best tool to do that one thing.