The PC game follows an alternative version of the Year Zero meta plot, so it will contradict the RPG in many ways. I would recommend playing the game and reading the campaign book to decide which version you like the most. There is a hint about the origins of the mutaded animals from the PC game that I head canon into the RPG, but that's a spoiler.
Another thing to keep in mind is that the PC game is based in Sweden and has many references to it, unlike the English version of the RPG which seems to have removed all references to Sweden (at least to my knowledge) (I haven't read much of the materials in English, so I might be wrong about this.). The Swedish easter eggs are hillarious, if you understand them.
The PC game does leave a lot of clues about the apocalypse that in the RPG only seem to show up in the background to the GM. I haven't used them myself in the RPG, but I would if I'd run that setting again. For example symbols on the artefacts and old texts.
When it comes themes, there's nothing I'd discourage you from drawing inspiration from. It's essentially the same setting with a few changes. Two differences I can point out is how the mutants understand the ghouls in the PC game, which they have a hard time doing in the RPG. The other difference is that the PC game revolves around the zone-stalkers and fighting, while the RPG has many other ways of playing and other classes. (The PC game shows only the stalkers going into the Zone, which in the RPG was the case until the start of the game, where other classes start going out with stalkers as guides)