I alway have had a doubt about how syndication works on Plone; AFAIK, to enable syndication site wide you need to create a collection; enable syndication on it, and the select it on the syndication control panel as the one to be used on site root:
what's the purpose of having the links duplicated? I think we must get rid of the one pointing to the collection or at least list it after the ones on the root.
they are different links to support different types of syndication formats. The formats that are supported are configurable per area you have it enabled.
IMO, I would even just completely get rid of having RSS from the root of the site. It seems mostly meaningless since you can't control order. By selecting a collection to display for RSS, you can control the content that is syndicated out to your users when they enter a url into rss readers.
Having the additional urls is harmless. Listing site root feed after collections makes sense to me as the site feed doesn't provide as useful of info unless you customize it.