I am not sure if we should do it this way.
GetWindowsBaseColor should do what it's name says. If we check for high contrast there and return something different it's not the windows base color anymore.
In which way does this fix the linked issue?

In order to fix another issue with HighContrast mode we should first search for an existing theme without an accent color. Because normally there is only one HighContrast theme (like in UWP).

Windows itself has different high contrast themes doesn't it? The settings app exposes 4 different high contrast themes on my machine.
If a developer chooses to provide high contrast themes and only want to provide two (one dark, one light) and does not want different ones for different accent colors they should just turn off accent color sync, shouldn't they?

If a developer chooses to provide high contrast themes and only want to provide two (one dark, one light) and does not want different ones for different accent colors they should just turn off accent color sync, shouldn't they?

We could, and maybe really should, check if we find a theme that has high contrast and the accent color and if we don't find any just choose a high contrast theme without the accent color. But we'd need some way to express this option. Not sure where and how we should add that.