It sounds like you have an unspoken assumption that only the web has that degree of flexibility. That's false, however.

The web platform gets around this by being flexible enough for the application creator to create a polished look and feel themselves, and ubiquitous enough for many designers and developers to know how to use it. That's also part of what makes it so resource intensive.

Smalltalk was flexible enough for anyone to create such a look and feel. Everything above the border of the VM itself was in the class library and was modifiable in Smalltalk, and most everything was in the class library. However, as a member of that community I can attest that many felt the need of this, but no one wanted to do it. Everyone who needed that level of polish was on a professional project and couldn't afford to devote that many resources to it, and everyone else was fine with the "developer" level UI.

The Web after the "Web 2.0" period grew both a developer and user culture emphasizing good looking interfaces with great UX. This was also increased by the aesthetics of smartphones and tablets after the appearance of the iPhone. The tools on the web are a bit less flexible than what was available to many earlier environments. However, there were more people with more motivation to make things look good.

It's not about flexibility and technical superiority. It's about numbers and motivation.