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.
MkI was the absolute best tool to do that one thing. Respectfully, MkII compromises on manual control to an unacceptable degree for my usage and an investment in education for beginners along with dumbing down the UI with explicit text labels (the font is indeed nice, but why do things with clean and clear iconography need these additional labels?) is not what I'd consider part of "that one thing". Of course, these issues could be fixed in the future, at which point I'd gladly eat my words.
I love Halide but I do wish it could shoot quick videos so I'd stop accidentally opening it and then saying "wait, wrong camera app." As-is I keep Halide on my home screen for pictures, and get to Camera through control center for video. But it's pretty frequent that I forget and tap on Halide thinking I'm going to record a quick video.
I'm not even talking about professional quality video, just "I want to record 5 seconds of my cat being cute." But I guess the reservations are partly that if you added basic video capability, people would expect it to be amazing in the same sorts of ways that it is for stills?
Halide's UI for things like setting exposure is faster for people who want to learn how to use it, versus Apple's stock camera being made for mass markets. And you can set more things, like shutter speed, instead of having it all be automatic.
You also get features like a live histogram and focus peaking that can help when shooting even if you aren't going to edit it afterward.
Can't try the new version yet because of an update bug, but I like the old version a lot.
That article waves away the manual focus, but for me it’s been very useful to manually focus when shooting through some near obstruction (ex: a fence, or low hanging leaves). There are also still situations where HDR falls a bit short and manual exposure results in a better picture (I have an Xs, so it might be better now).
It gives full manual control, live histograms, and a nice one-handed interface. I'm not sure what you get for free, and obviously whether the upgrade is worth it is up to you, but I bought the full unlock when it first came out and haven't regretted it.
"Full manual control" is somewhat crippled in Mk II (it switches back to Auto every time I switch back cameras) as well as removing the ability to pin ISO down when making use of tap autoexposure (there is no option but to have both exposure length and ISO adjusted now). Manually adjusting exposure length also sometimes leads to it getting "stuck" on long values like 1/2 or 1/1 far longer than Mk I ever did. I get that they think their new Auto mode is better, but in general this was a bug-infested and unwelcome surprise update for my usage of the app (getting maximum quality raw images out of my phone mounted to a small tripod.) None of this would be an issue if I had any way of opting out of this generous "upgrade" I couldn't refuse. UI fit and finish has also degraded significantly from my subjective POV and the large potential scope of future feature updates make me pessimistically assume that the app will continue to fail to be particularly well tested. If the devs are still listening I'd gladly pay (again) just to have the MkI app back, if money is what they want.
Browsing the spec sheet, IF it floats your boat, this feels a useful option:
"Halide’s Depth mode lets you capture Portrait mode shots of pets and people — even if Apple’s Camera app can’t. "
That feels it makes it more similar to my Samsung where I can choose what to "Live focus" on and create fake depth (although I feel Apple's people-only system allows them to recognize and transition borders better)
The only real advantage to shooting raw on your phone, is that all the hdr processing tends to flatten out the global contrast between dark and light regions. If you shoot raw, you can get a more natural photo with less processing.
Even shooting raw with this app, I just use the auto exposure and auto focus.