The solution to sync this correctly (or at least, the best one I have found so far) is to watch to the theme state change of the app, then query for `meta[name='theme-color']`, and set manually its `content` attribute to your desirable colour.
The theme colour you declare in the manifest and `<head>` of the html index is more of a fallback than anything.
I'm sure you'd figure it out, but let me know if you need something more detail; I would be happy to help.