In terms of a specific project, not really. Look at everything that goes into an environmental study: watershed/water quality, affected wildlife/endangered species, noise & vibration, soil contamination, archaeological issues, visual impacts, rodent/pests, etc, etc. On top of that, you have to consider the effects of all of those areas during construction and ongoing operations for 20+ years. And that doesn't even account for NIMBY issues.

When you're getting into the details of a specific project, it can quickly become overwhelming, especially if you have people who may be philosophically opposed to the project hammering you with those issues time and time again.

Are they factoring to build it with pollution and no safety when they estimate the cost and schedule these days?

When you look at a project at a high level, you make general assumptions, but as you get more detailed and you know specifically what kind of equipment

Take for example, tunneling: At the start of a project, your best information tells you that the sand down to 70ft below grade is clay, so you make your cost and construction estimates using this assumption. You get into detailed design and send drill crews out to collect sample borings and you find out that in much of the area where you assumed sand, you actually have bedrock coming up to 10ft below grade. Now you're plans have to change - instead of doing cut-and-cover tunneling everywhere, you have to blast in some sections, which means having to get a blasting contractor, deal with protecting nearby structures, changing traffic patterns to allow for the blasting etc. In the old days, the project would have just blasted, and if someone's foundation got cracked in the process, too bad. Today that won't fly.

edit: just saw your edit

In fact, if you read about the history of Hoover Dam there were a number of these things that they weren't legally mandated to do back then, but did them anyway.

Compare the number of people killed at the Hoover Dam project compared with the number killed during the Big Dig.