Once opening the customize buffer all checkboxes are selected by
default, even if they were de-selected by the user previously, which
means that the user may unintentionally change settings they didn't
intend to.

Emacs -Q -> M-x customize-face -> default -> deselect
Foreground/Background -> click Apply. Close the buffer, then open the
customization again. Note that the foreground/background checkboxes are
selected again.

The result of this is that using the customize buffer may have
unintended side effects. In my case, I opened the
customize buffer only to change the font, but accidentally defined a
foreground and background color in the process which led to some themes
breaking. This is most noticeable when opening the customize buffer when
using a light theme, saving, then loading a dark theme. For example
modus-operandi/modus-vivendi.