Don't worry about it, not a problem with poking your eye out. Long action or magnum actions have been around for 50 years and nobody has complained of your concerns. The bolt is not in line with your vision, should be a couple inches below line of sight.
It’s not like a long action is a Red Ryder BB gun. Besides, if your concern had any validity, the State of California would have already required a warning on the rifle.
I built one on a long action M700 and had zero problems. It's really not that much difference - only 0.66" in a Rem 700. Same action length as a .30-06, .300 WinMag, etc..