Supplementation pages are just additional pages that can be associated with your normal wiki pages by a link in the theme.
One usage of this feature is to have one "discussion page" in addition to each of your wiki pages. Then each wiki page will have a link to the "discussion page" by default.
A wiki administrator can choose to enable this feature for all pages by putting this into wikiconfig:
supplementation_page = True # default is False
The name of the supplementation page and the template used for these pages can be set like this:
supplementation_page_name = u'Discussion' # this is the default supplementation_page_template = u'DiscussionTemplate' # this is the default
A wiki user can control if he wants to have the supplementation feature on a per-page basis by using a processing instruction at the top of the page content:
#pragma supplementation-page on
Usage with off disables the feature on that page.
Separating discussions / comments also has some negative impact as you will have to provide context. If you don't do this, it might be unclear to what you are referring. If you could just comment near the context you are commenting, it would be less clean, but somewhat clearer/easier.
There is only one fixed supplementation_page_name (default: 'Discussion'):
There is also another, quite different "commenting feature" described on HelpOnComments.