The preference for native look was once about the impact of familiarity on usability. When 95% of people's interactions with computers was a single OS and native apps, they would expect controls to look a particular way. They could figure out other variants, sure, but from a UX design perspective, there's little reason to add that minor cognitive overhead needlessly.
Today, people's experiences are less likely to be monoculture like they once were, which dilutes one of the values of native controls. That's not to say designing with familiarity of controls in mind doesn't have value, just that it's less about, for example, buttons looking like buttons native to the OS, and more about visually reading as "this is a button" more generally.