Perhaps the reason Alex goes to such lengths to protect his mother from knowing about the changes might have been, in fact, not simply the direct shock of the changes but also to prevent her from recalling the traumatic events that led to the heart attack in the first place (seeing him being brutalized by the police during an anti-regime protest). Seeing the changes might remind her of the difficult and traumatic events which led up to those changes. It's possible that he also has some sort of survivor's guilt or similar, given he was unable to help her due to his arrest and managed to escape with nothing but a beating. It might be that he doesn't admit this directly and not realizing this why the rest of the family think he's a bit crazy.
Even though Denis' The Matrix T-shirt was worn because of a deleted scene in which Denis outlines his plans for a Matrix-like film called Planet of the Forgotten, it still fits in with the finished film because what Alex does is almost like a non-digital version of the Matrix's simulated reality; when his mother walks outside for the first time and sees the changes, it's pretty much the equivalent of Neo's waking up from his capsule.
