There are tons of behind the scenes pictures and video of the Rocky puppet being used on set, and Andy Weir talks in interviews about how almost no CG was used to enhance the puppet. I guess it's possible to fake all that, but it's a lot of lie to cover up.

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