* CLI tools present in my terminal's specified fonts and colours. Near total control. The main exceptions are ANSI escapes, and even those I can limit to black-and-white -- usually normal, bold, and reverse-video.
* Most desktop apps integrate into some desktop enviornment (or environment(s)) for font size(s), colours, etc. OSX is actually something of an exception, which I realised when trying to see how I might set that up for a visually disabled friend.
* Even where desktop apps don't have systemwide configuration tools, you're generally seeing the same toolkit (or limited set of toolkits) in use. Most of the experience is highly uniform.
* Straight-up text presentation is typically quite good. Far superior to Web tools.
They let you change colours, typefaces and shapes slightly. You could do that with Windows 1.
That's not the same as what CSS allows (complete reconfiguration).
Yet you say you miss native apps, which absolutely dictate everything about how they work?