Hi Lauren,
Yes, I’d expect those things you list to be included. Fireproofing has a noticeable impact on embodied carbon and should be included if code requires it for steel, and the concrete topping for shear and acoustical mat on mass timber should be included if they’re likely to be needed.
I have heard the contractors often estimate secondary steel by adding 10% to the primary steel estimate early in design, so that might be a good way to cover that. In Tally you can add a multiplier to each assembly if you want.
-Kjell