Yeah, the proposed cut-through of the Cobb building is definitely clunky, and I'm not sure what the point is.
If you want to draw people in from Congress Square to the sculpture courtyard, a more productive and less destructive approach would be to improve the High Street sidewalk, instead of trying to make this quasi-private alleyway.
It's also sacrificing a lot of interior floor space for the museum's galleries (what's going to happen with that weird leftover space between the arch and High Street?), and I don't think that the historic preservation board is going to love it, either.