Great question, David. I don't know that I've ever come across any methodology (outside of sales) that really focuses on managing the human side of business. Too frequently we're expected to spend more time measuring performance so we can't really look at managing the "people" side of getting the work done.
I think the biggest contributor to the kinds of issues you raise regarding scheduling and estimation is twofold: Having decades of history to overcome, and a lack of trust. Construction is probably more prone to this because, as a contractor friend once confided, "Contractors are never on time and it will always take longer and cost more than we tell you."
Having spent a few summers as a construction laborer back in college, that seems pretty accurate, and I'd imagine everyone involved tends to pad their schedules and estimates accordingly. When you're looking at a large project, the sum total of the subcontractors padding adds up pretty quickly and must make it impossible to accurately manage to a completion date. And even with all the padding, nothing ever seems to get done on time!
The trust factor is huge here, requiring commitment by both the GC and the subs to be as accurate and honest as possible when estimating their work and then trusting that everyone else will do the same and work to that schedule. When I was given my first promotion to a management position, I had no idea what I was doing and my team figured that out pretty quickly. One of the best books I read when I was learning the ropes was The Complete Idiot's Guide to Leadership.
No self-respecting professional would have an "Idiot's Guide" or "Dummies" book on their bookshelf so I kept it at home, but it focused on becoming an effective manager by building the trust of your team rather than relying on numbers, meetings and arbitrary mandates to run the show. While it might be a little rudimentary for someone who has been in a management position for a while, the attention it pays to the people skills required to be an effective manager might help put a fresh spin on more metrics-focused management theory.