Basement concrete leveling issue for click lock hardwood flooring installation
Assuming that the issue is a bulge in the concrete, I'd be fixing that first. You cannot lay wood flooring over that severe of a bend. Either break up the hump and remove it, or cut out the entire area and refill with concrete. 

You'll want to shorten the pipe and install a cleanout plug (threaded fitting). This should be slightly below the surface of the concrete. You can then install a stainless steel cover after the flooring is installed.