I can make a forced analysis of System Shock 2. Starting also with the broken pseudo-maternal AI that guide you through the first half of the game before spoilerspoilerspoiler.
Within my limited experience with talking to artists and poets, I don't think artists deliberately set out to include specific symbols inside a work. Too much left-brained stuff. Which I find funny as a deconstruction essay requires you to spell out exactly what it is you are talking about. Kills the mood.
Yet most artists that are any good at their craft easily tap into something that hits you in the gut. I think Portals is one of those games. I have not played it, but I bet it does mess around in your head in ways beyond just messing with your sense of space-time. I wasn't too hot on playing it, however, after reading the article, I want get a copy now.
The idea of analyzing Valve games critically is pretty good, though. They're one of the few studios which makes games worth analyzing! I'd like to see articles like those.