I thought that effect occurred (only?) in lenses with "internal focussing" (the lens barrel doesn't move when focussing, but internal elements move). In such lenses, focusing is done by changing the focal length at inifinity of the lens. This has nothing to do with variable focal length as in zoom lenses (which change the angle of view by changing the focal lenght
at infinity of the lens).
As for the marked focal length on a lens: as always, this is the focal lenght for subjects 'at infinity'. In the simplest case, getting closer to your subject means moving the lens away from the sensor (see e.g.
http://en.wikipedia.org/wiki/Lens_%28optics%29), and the closer you get to the subject, the farther away from the sensor. So the minimal focussing distance depends on how much the maker wants to invest in longer barrels, and longer gear paths or more precise steering.
For lenses with internal focussing it's a bit different (the lens barrel seems not to move), but there also, closer focussing distance means more expensive construction, and might hit optical limits (distortion and aberrations getting out of hand)