How to identify Windows 10 background store processes that have non-displayed windows that are programmatically visible and minimizable?

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The approved way of detecting these phantom windows is to use DwmGetWindowAttribute and DWMWA_CLOAKED.

Here’s the code I’ve used:

static bool IsInvisibleWin10BackgroundAppWindow( HWND hWnd )
{
    int CloakedVal;
    HRESULT hRes = DwmGetWindowAttribute( hWnd, DWMWA_CLOAKED, &CloakedVal, sizeof( CloakedVal ) );
    if ( hRes != S_OK )
    {
        CloakedVal = 0;
    }
    return CloakedVal ? true : false;
}

Thanks to Scot Br from MS for posting the answer here

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