I think railroads typically had an engineer on their staff back in their early days, along with surveyors and in the case of Union Pacific, a whole construction company.
Stewart
Railroads don't go in the builder box. There's a category for bridges that were built by railroad forces. Most bridges weren't built by those forces, and several of the bridges you've put the railroad in the builder box for were built by other manufacturers.
I can't tell you who built this one/Bored the other tunnel, but I can tell you that the Pittsburgh Railways trestles were built by others.
A couple of the ultra-early railroads had their own bridge shops (B&O and Reading are two known examples.), and the Milwaukee Road liked to do some construction in-house, but for the most part, bridges were/are contracted out to other companies, not done in-house.