I couldn't agree more -- especially when the job is a more researchy role. Right now, I'm at my first "real job", a research internship during my PhD program, and the contrast between my productivity at school and here is shocking. The need to clock in and out and the desire to "look busy" all the time actually end up hurting my productivity, I think, much more than helping it. When my responsibility is creative thinking and new research, much of my productive time is spend doodling in a notebook or staring into space. While sitting and coding is important too, I don't feel like the normal metrics for the appearance of productivity apply.
So, paradoxically, I get paid for the time I sit in my office and begrudgingly hammer out code; the time I spend at home coming up with the important ideas to drive the research goes pro bono.
Maybe I'm just lazy, but I really think that sitting in a windowless office for eight or nine hours a day is not the way to encourage maximum output. Personally, I find myself thinking I'd be much more productive if I just "worked" a little less.