Currently, I know of the following options, which don't satisfy me:
- I could just download Factorio from the website and use that, it will not retrieve the Steam achievements. However, I would like to play it on Steam, and I would like my play time to be updated there (so I can't just add it as a non-Steam game; also Steam auto-updates, a downloaded version doesn't)
- Use a tool to reset the achievements in Steam itself, but then the first date that I earned the achievement will be lost as well.
- Replace factorio.exe in the Factorio game folder with a non-Steam one (eg. from the website download), so it will track on Steam as usual (play time, etc), but won't integrate with steam (ie. won't download achievements). It would be replaced on the next update, though, and is pretty hacky in general.