I have seen users having trouble with pixel soup UIs. They may not think "This should be in a native toolkit", but they do think "How the hell do I subscribe to a folder in the new Outlook?".
The problem in these usability cases is pretty much always layout and constant redesigns rather than the exact theme the button has. I've seen plenty of unusable native ui soup UIs and very clean and simple custom UIs.
You could call it the exact theme when a clickable UI element looks just like regular text (it was not inside any kind of button-like shape in the Outlook case that I saw), but it's super common to have that in web-based UIs.
Right, but bad UI's was not uncommon before webviews, if anything the spartan-ness of the web often simpified patterns whilst reliance on weird hotkeys in desktop apps isn't uncommon.