Contrary to what has been told to you and the marketing hype from Zodiac the Nature2 will NOT allow lower FC levels in practice. It is merely a very expensive algaecide. Plaster finishes (and pebbletec is a plaster finish) are prone to staining from metals. Period!
As far as problem with the autocover and a SWCG, if everything is properly bonded it usually is not a problem (assuming the cover is made from material that are resistant to salt, which might cost a bit more. If it can be installed in a coastal community such as the Florida coast it should stand up to a SWCG.) I would be more concerned about problems with trapped chlorine gas and volatile chloramines taking their tole on the cover than the salt in the water. Check with the manufacturer of the cover and see what they have to say.