The shell's background is not the scheme's background

A desktop shell is usually a window colour with rounded panels floating on it. The panel is not colorScheme.background — it is one shade back toward the middle, so it reads as raised:

// adapted — resolved INSIDE the theme, so MaterialTheme already holds the resolved scheme
val isLight = MaterialTheme.colorScheme.background.luminance() > 0.5f
val windowColor = if (isLight) Color(0xFFFFFFFF) else Color(0xFF000000)   // the extreme
val panelColor  = if (isLight) colorScheme.surfaceContainer else Color(0xFF121212)  // one step back

Scaffold(containerColor = if (isDesktopShell) windowColor else colorScheme.background) { … }
// … and the content area, deeper in: .padding(8.dp).clip(RoundedCornerShape(12.dp)).background(panelColor)