If it's a company that hires union workers, it's really tough for anything hinky to go on in payroll because the union will be watching everything.
Depending on the size of the company, yes there could be shady stuff in payroll, and yes in a small enough company anyone who sees the books might notice it and know about it, but it would have to be a very small company and the person looking would have to know what they're seeing. Have you ever seen the paperwork associated with payroll?? It's gobbledygook if you don't know what you're looking at. You couldn't just spend five minutes in someone's office and suddenly know that they've been running two sets of books.
Where I work (mid-sized construction company) the closest the site will ever get to payroll is filling out timesheets. They code the hours to the work and send them in. Payroll gets them, project manager gets them, and coordinator/engineer gets them (first one to pay the workers, last two to do cost control and make sure everything is coded properly and tracking within budget). After that, the super and site engineer will have nothing at all to do with payroll.
A certain amount of "horse trading" as I've heard it called, goes on on site between the superintendants of the general and the various trades, but it's usually just so they can avoid dealing with the paperwork. Carpenters do the layout wrong, so the electricians have to do a bit of rework... instead of paying for the rework, the carpenters build an enclosure that the electricians would have had to order/build themselves the next month... that kind of thing.
Construction can be a marginal business at times, particularly since it has such a reputation for being run by "
legitimate business men". The latest big thing is 'cost plus', in which we hand over our books for the project (every purchase, every timesheet, every subcontract) and get the cost of that plus an agreed mark up. Really kinda tough to do anything screwy with the cash flow in those conditions.