Since you’re concerned about the legitimacy of your Steam Achievements list, I would strongly advise you do not mess around with an unofficial editor, that has no guarantee of not messing something up. That’s not a dig at the author of that editor, not anyone who uses it. Simply that it’s not official, and if anything goes wrong (user error included), Funcom/Valve will certainly not be helping you.
Do you know how/where to get that specific achievement? I won’t mention any spoilers here, unless you request them. I would suggest just going through the motions that would have given you the achievement, and then you would have still earned it.
Just my opinion, as someone who would feel the same way as you do if I was in your situation.