Thank you for trying so hard to reproduce this issue! I am using the "New UI" option in Rider and also the "Sync with OS". Also I forgot to mention, that I used the OS settings to switch from light to dark theme when I noticed that NCrunch continued to use the light theme.
Today I explicitly switched themes from the Rider settings and everything worked as expected, i.e. the NCrunch theme was always in sync with Rider. Then I reenabled the "Sync with OS" setting and repeated switching themes via the Windows OS settings - and... suddenly NCrunch and Rider are still in sync!
I will continue to observe this behavior, but at the moment I don't see any need for action on your side. 🙏