What's a "constitutionally small penis"?
"Constitutional" refers to the physical state of the concerned individual (Merriam-Webster). 

In biology, it most probably means a trait that is not pathological or environment induced.

This is in the context of size of babies:


  Small for gestational age (SGA) can occur following a pathological
  process or may represent constitutionally small fetuses.
  
  From: Ananth &amp; Vintzileos (2009)





  Between18-22% of infants SGA by population
  standards are reclassified as normally grown by customized standards
  and as the perinatal mortality of these reclassified babies is similar
  to those who are normally grown they can be considered to be
  "constitutionally  small.".
  
  From: McCowan et al. (2018)





  In most cases, it is difficult to differentiate between
  constitutionally small head size vs pathologic microcephaly, and
  available data regarding prenatal diagnosis of microcephaly are based
  on small numbers of cases of varying etiologies.
  
  From: Ultrasound screening for fetal microcephaly following Zika virus exposure.
   American Journal of Obstetrics &amp; Gynecology, Volume 214, Issue 6, B2 - B4


 

Regarding constitutionally small penis: Since the article you mentioned is the only source (scientific or otherwise) of this term, I would believe that it is based on the population average (of possibly South Korea from where the authors are). Moreover, since it is not defined rigorously, it is most likely an arbitrary classification.