I like that Jonathan does things his own way. He doesn't need to care about competing with Photoshop, etc.
Personally I find layers encourage me to over-process. These days I'm using Affinity Photo, which is kind of a Photoshop clone, on my iPad. So while it has layers I don't use 'em.
-Dave-
There are different needs for different purposes. I tend to agree with you that in some cases, layer incitate to over-process
And not always necesary.
But as Rhossydd said, the lack of layers limits a lot the range of potential users. If layers are disponible, we can or not use them but there is the choice.
Layer based workflow is inescapable in many areas of photography but also key for a branche of digital artists who use photography as only a part of a much wider process, it is not photography any longuer in the strick sense but digital imagery, so to say.
At least 2 high-end motion softwares could be considered as layer based, Baselight and Mistika, and in compositing we find the After Effect approach also based on layers. So many many people are manipulating layers at one point or another in their workflows.
In my case I never ever use a Lightroom kind of software because I don't shoot Raw but 100% layer based PS in PSB or EXR. (Less) and a few other softwares to roundtrip with PS, but I'm not doing stricktly photography. It really depends on the needs and if someone never uses layers, it's fine they have alternative options.
Affinity Photo is quite good by the way and a serious PS alternative.