It was always the wild west. Windows was full of "native" apps that reinvented their own UI. Off the top of my head:
- Office (custom widget toolkit, menus, toolbars, etc)
- Internet Explorer (frequently introduced new toolbar designs not available to apps via API until later)
- Encarta (custom dark mode-ish theme)
- Netscape Communicator (custom toolbars)
- RealPlayer
- QuickTime
- MSN Messenger (custom theme)
- Every video game ever
... UI inconsistency didn't arrive with the web. Even macOS has always been a patchwork. Apple couldn't stop introducing new themes over time and there were always apps that didn't quite follow. Brushed metal!
Kai's Power Tools / Power Goo / Bryce took the custom interface stuff to the most extreme lengths - people genuinely loved it at the time but I think most would be horrified if anything went that far today.
https://mprove.de/script/99/kai/index.html
For all those instances, at least keyboard navigation worked. Modern UIs are impossible to use with the keyboard.