I would argue that in many cases these kinds of things are management choices, too. As an example, I'll use my dad who works in a more traditionally blue-collar local government union job doing construction work. When I was young, he busted his butt building stuff, now near retirement he spends much of his time "standing around doing nothing" - however, this comes down to outsourcing and lack of hiring.
All large projects now are outsourced (this gives the opportunity to graft, and may or may not actually reduce cost). However, they still need a skeleton crew of actual staff for projects that don't make sense to outsource short of contracting the whole construction function: fix a broken window, paint a wall, hang a door, change a broken window AC unit. Now, he may have one or two such hour-long jobs to do in a day, and he is able to spend most of the day "standing around doing nothing" while completing every request on time, and he's not exactly rushing the work.
Perhaps the main root is that the governance structure diffuses responsibility. When the governor is asked about problems at the MTA she points out that she doesn’t have full control of the agency and that’s true. Nor does any other elected politician.
But if we go beyond the root causes and look at the proximate causes—yes, that includes understaffed and incompetent management, too many contractors picked and supervised via a terrible bidding system, lack of cooperation from other government agencies, excessive litigation costs—-but also union/civil service featherbedding.
The people that live here see municipal workers standing around doing nothing. We read about those gaming the overtime system and building secret clubhouses. We know about rubber rooms where teachers sit for years while the process to fire them plays out.
A famous New Yorker once wrote a book titled “Don’t pee on my leg and tell me it’s raining!” That’s basically how I feel about the unions in NYC.