A (man+box) measurement will be less accurate than a simple (box) due to the propagation of measurement errors. In the (man+box) case you are doing two measurements compared to a single measurement in the (box) case.
$Man = 200 lbs$
$Box = 50 lbs$
$Scale = \pm0.5 lbs$
$Box Measured Weight = (250 \pm 0.5) - (200 \pm 0.5) = 50 \pm 0.7 $
In this example the box weight has more measurement error than if we just measured the box weight directly. Depending on the scale error and the box weight relative to the man, the final error can be large, for example:
$Box = 5 lbs$
$Scale = \pm 5\%$ (a really bad scale, probably not realistic)
$BoxMeasuredWeight = (205 \pm 5\%) - (200 \pm 5\%) = 5 \pm 14 lbs$
If we just measured the box directly the error would have only been 0.25 lbs.