^ The cost of doing an all glass dome like that would be spectacular, particularly because the structure would require a certain aesthetic. You can see the as-built structure is pretty chunky, and exposing that wouldn't be pretty. I'm sure they saved big bucks making the dome solid.
What would help is to shoot lighting up at the dome from below...inside and outside. It will completely eliminate that nasty tunnel effect. I'm 100% sure they will do this. Right now the interior looks dark without all those finishes and lighting that are major part of this space.
I guess (the point) of doing a glass dome is it was such a major part of the design. The MTA was probably very happy with that feature, and still wanted it around, even if it went opaque. Very common that clients will like certain features of the architecture, but a material swap is sometimes required if cost becomes an issue. Not sure if that's the reason, but just saying I see that alot.
I wish there was a glass dome too. The disappointments of value of engineering.