In general I agree with you. As a puzzle game it is outstanding but the story just leaves players dazed and confused. I've read some Blow interviews and various interpretations and the game, while very well thought out, simply does not intend to lead the player to a specific outcome. Blow used every literary device in the book but in the end couldn't make a single recognizable point.
It makes me sad that the final level has one of the most brilliant videogame twists I've ever seen but ultimately it leads nowhere. If only the game had solidly been about a man reconciling a lost relationship with no mention of the Manhattan Project.