Why can?t transpiration measured in a cuvette be used to evaluate
total canopy transpiration?

If I had to guess, it would be that capillary action in plants is
different from capillary action in a glass cuvette.  The little
capillaries in the plants have different geometry and different
surface properties.  How exactly plants do what they do is still an
active area of research.  Abe Stroock at Cornell is one person working
in this field:
http://www.cheme.cornell.edu/peopleevents/faculty/stroock/Research.htm