The current behaviour is:
If you have checked that option, comments are enabled for all the pages, whether “Allow comments” is checked or not.
If you have that option unchecked, comments are disabled for all the pages except those for which the option “Allow comments” (edit/quick edit) is checked.
I see your point CI Media, but IMHO shouldn’t be removed, but this notice:
If checked, this option will enable comments on pages. You can disable comments for a single page in the quick edit mode of the page list screen. Change other comments settings in the discussion settings page.
should be:
If checked, this option will enable comments on pages. When unchecked you can enable comments for a single page in the quick edit mode of the page list screen. Change other comments settings in the discussion settings page.
So the real problem is that that “Allow comments” checkbox, is checked by default (wordpress, not theme related) but one might not know it, also because previous Customizr versions overridden that option.
Also consider that, when that option is unchecked, basically Customizr doesn’t do anything else that picking up the WordPress option. So when unchecked that option is “transparent”.