Yes, that's expected and since the only thing that mattered for the purpose of viewing the video in the article was orienting the linear polarizer towards the computer screen, I omitted the details.
Here is the explanation.
3D projectors normally use circularly polarized light because this method is insensitive to head movements and tilts which would lead to unpleasant effects if they were using linearly polarized light instead.
The different images for both eyes are projected with clockwise and counter-clockwise circularly polarized light.
The glasses first convert the circularly polarized light coming from the cinema screen (these are special screens that don't mangle the polarization) to linearly polarized light which is then going through a linear polarizer, eliminating the unwanted polarization. The filter for the other eye eliminates the other polarization which allows to target the left and right eye individually.
Because the glasses are built like this, the linear polarizer has to be towards the eye and therefore we need to turn it around for us to work here. It doesn't matter for the eye that the remaining light goes through the quarterwave plate by the way.
(I'm not sure why this technique works with different colors at once btw!).
