The problem starts when you want to ship to every device known to man but you only have the dev power to maybe ship it to the web—enter, Electron (and all that other similar crap).
Don’t blame it on the designers or the developers. This comes from above the worker bees.
There's a document I've seen floating on the Interwebz, a copy of HIG for ancient Windows version, I think one of the 3.x ones. I distinctly remember it for having a note somewhere basically recognizing that giving some of the theming/customization options in the API is a bad idea, but customers want to brand their apps, so what can one do.
This is one of the problems that I can't see being solved, because it's purely social - we'd have to have someone go and tell every entrepreneur out there that branding is a fucking stupid idea and you should not do it, and actually be taken seriously.
I can't even imagine a world in which that is possible.
Yeah, you lose some people with a shifting target, but it's easier to make them swallow 1% different every month than 50% different (to a competitor) all at once.