@mk0r I can’t reproduce this problem here on Meta. I use the Grey Amber theme/color scheme here which isn’t the default theme for Meta:
And the theme-color meta tag has the right color for me:
<meta name="theme-color" content="#36393e">
#36393e is the header background color of the Grey Amber scheme. If I open Meta in an incognito window without logging in, the theme-color meta tag has the header background of the default color scheme (the Light scheme):
<meta name="theme-color" content="#ffffff">
Have you tried cleaning the browser cache/cookies for your site? If that doesn’t help, can you try and see if you can reproduce this issue here on Meta and share the steps to reproduce the issue?