Andy Weir is a wonderful novelist and was truthfully relating his understanding but he's not a VFX person.

I didn't see the quote you did but he probably confused the fact that PHM used physical elements in place of some CGI in certain scenes and the separate fact that a realistic physical puppet was used on set for reference. Some parts of that puppet are seen on-screen in some shots but most of the creature in most shots was CGI or CG enhanced (which looked great thanks to the ideal in-camera puppet reference it replaced). I explained more here: https://news.ycombinator.com/item?id=48198851