I too saw the same set of warnings when building the project (Vivado 2014.4 on Windows 7 64-bit). Taking the advice to ignore warnings on the blog post, I copied the newly built bitstream file to the SD boot sector and fired up the Parallella. The board booted and Epiphany examples run without a hitch.
I'm new to Vivado and my ISE experience dates back to 12.4, so I can't provide details on your other questions without consulting the docs and knowledge base, but at least the answer to #2 is Yes!
Cheers,
~ Mark