I found an open Github issue regarding the same subject. It looks like you can’t set Brave’s title bar color to match with Windows’ colors as of the moment.
I also liking the new update of brave… its looking awesome… but your request is actually normal bahavior since its the default of brave browser… but you can actually change the browsers header color by chaning theme by installing it in the chrome web store. You can try brave dark theme, its a lot nicer look and easy for the eye.
Guys, OP wants the title bar color to match Windows’ colors when Brave colors is set to Same as Windows. Changing colors and themes isn’t a solution to OP’s request. Brave developers are aware of the case and they’ve included the feature in their plans, as you can see from the Github issue above.