The explosion of JS apps is a cost saving measure for vendors that given real choice, I don't think many consumers would opt for. The point is once you have lock-in and network effects, your customers don't really have much of a choice in the matter. At the very least, you can't say that's the market speaking in favor of the substandard apps any more than you can say it's the market speaking for any other choice the vendor makes.
As a related example, I'm sure people that were using 3rd party Twitter clients aren't feeling like the market has spoken and the best app has won just because Twitter killed off their API access. Their choice to stay on the platform has nothing to do with the their new-found love of the official apps.
The Linux point is interesting. I have a Linux workstation I use regularly (in addition to a macOS laptop) and sometimes the desktop integration is nice to have. I just also struggle to believe a company worth 10s of billions building tools for software developers couldn't solve the problem in any other way. It feels a bit like we let companies off the hook. Whatever misgivings people have about the UI consistency, we have plenty of Linux desktop software that runs well and developed on far smaller budgets. I could live with resource-hogging vendor software if there were open protocols or APIs in place to supplant with something of my own.
That's quite literally the market having a say.