Consider rigging up a temporary ”roof” (use poles and a tarp or something like that) over the 2nd story deck so you can see the new reduced view from the 3rd story windows which will be overlooking the roof. Also check the reduced light into the 2nd story of the house.

Perhaps a retractable awning(s) over the 2nd story deck is a compromise solution.

I would suggest retractable awnings instead. Adding an enclosed porch room will really kill all the light getting though the sliding doors.

Someone on this forum just added a roof over their patio and was so disappointed that when they looked ou their windows on the floor above, all they could see was roof.

https://www.houzz.com/discussions/6489600/patio-s-metal-flat-roof-visible-from-living-room#n=27

Can you imagine how dark it now is inside the house because the low patio roof kills all the light.

I am guessing the deck on the lower portion isn't waterproof, so that would need to be addressed. The upper would be difficult with the windows so close

Have you discussed this with an architect? I can see the want, but a major overhaul may be the only solution the overall elevation is limiting, not to mention how a roof on each level will darken the interior spaces.

I think you'd have to go big: a 2-story tall space with the roof tieing in to the upper roof. It would be spacious. Search for "2 story screen porch". Youll find some examples.

Could you scale down the project and just think about a 3 season room on the bottom level? I would think next step would be selecting an architect for the project

Te roof will have an effect on the view on the top deck . The idea of the retractable awning IMO is the best idea . That lower area is a dark hole and now you want another one .? Imo enlarge that lower patio add some umbrealls and enjoy the view . Maybe even a fire pit .