Most likely has an option for what slot to boot from
On the topic of cards using it. Cards get faster with every release and sometimes you get dual gpu on one card setups(so having extra bandwidth is great for those crossfire/sli on a card setups). For sure you will be able to put that pci-e 3.0 slot to use in the next 2-3 years if not sooner.
Today's main stream cards are getting nearly as fast as 2-3 generations back high end cards, so even those will get the advantage with time.