I'm not sure they're saying that end-users shouldn't make those decisions, simply warning that customised versions of their software won't be supported by upstream to the same degree, and thus distributers should leave the styling as-is. On the first point, to quote the article:
"If you like to tinker with your own system, that’s fine with us. However, if you change things like stylesheets and icons, you should be aware that you’re in unsupported territory. Any issues you encounter should be reported to the theme developer, not the app developer."
I think that's the point they're trying to make - there is a certain amount of caveat emptor associated with theming. But they don't make it well when they say "don't them our apps".
"If you like to tinker with your own system, that’s fine with us. However, if you change things like stylesheets and icons, you should be aware that you’re in unsupported territory. Any issues you encounter should be reported to the theme developer, not the app developer."