Desktop GUI toolkits aren't less flexible on layout, they're often more flexible.

We lost it because the web was never designed for applications and the support it gives you for building GUIs is extremely basic beyond styling, verging on more primitive than Windows 3.1 - there are virtually no widgets, and the widgets that do exist have almost no features. So everyone rolls their own and it's really hard to do that well. In fact that's one of the big reasons everyone wrote apps for Windows back in the day despite the lockin, the value of the built-in widget toolkit was just that high. It's why web apps so often feel flaky and half baked compared to how desktop apps tend(ed) to feel - the widgets just don't get the investment that a shared GUI platform allows.