InDesign lets you determine where the stroke is located on a box or shape. In the middle of the stokes palette is the "Align Stroke" option. By default, the stroke is centered on the path. So a 2 point line with have 1 point outside the box and 1 point inside the box.
With thicker strokes, the placement of the stroke really matters. Below are three boxes that are drawn to be exactly the same size. The only difference is the alignment of the stroke.
It's helpful to use these settings when you are trying to get precisely measured shapes. I use the inside alignment option all the time.