In the dark theme --color-border was #262626, identical to --color-secondary/--color-muted. The global `* { border-color: var(--color-border) }` rule therefore rendered borders invisible on those surfaces - e.g. the folder sidebar's right border and the account header's bottom border vanished in dark mode.
Set --color-border to rgba(128, 128, 128, 0.3) (the same neutral the navigation rail already uses inline) so borders stay visible and consistent across all dark surfaces (background, secondary, card, popover).