Well, I see a few potential problems from what the drawing shows.
Mind you, first off, you should discuss your concerns with your architect, as that may be the way to get them addressed, or to get your architect's view on how the design will work. Unfortunately, as I recall too well from a Frank Lloyd Wright exhibit, sometimes architects think things like roofs that leak and chairs that fall over are not their problem. You should ask to visit & interview the owners of built examples of any prior projects with a similar feature, if there are any.
So - looks like a totally flat roof, which will almost certainly leak. Looks like a glass box with the upper part unventilated, which may serve as a place to do some low-grade solar cooking, but otherwise might be a lot hotter than you want much of the year when the sun is shining. When the sun is not shining, it may be quite cold, or require a lot of supplemental heat, much of which will be wasted. Not sure what the climate where you are is like.
Presumably the idea is to bring light into the building through the stairwell, but this seems like an extreme (and probably expensive) approach to that goal.
I would expect you to have a number of dead birds scattered around the building on a regular basis, as well, with that "glass box sticking out" arrangement, where they fly into the glass thinking they can fly through. Using frosted glass where the view is not a factor could help to reduce that.