The game was all ready won (obviously) since I had to colonize roughly 250~ planets to get all of the artifacts so I'm just going to assume that that's not the issue.
Actually I think it is the issue, but not the way you think it is. Achievements that are not won by doing X at the end of the game are actually given to you the moment you meet the criteria (AKA own 12 different artifacts), not on game completion. However, I think this only counts for games still going on. Once you get the victory screen I don't think the game still checks for achievements (since you're not really fighting with anyone anymore). Granted for this particular artifact, that makes no sense, but it is what it is.
There is certainly nothing wrong with using the GalaxyForge duplicate your favorite nonrandom map with 100% artifact density to get this achievement, especially after you've technically already done it. You can also just manually change the achievements file but that's no fun.