For me, it depends upon my purpose for using each product.
If I desire enduring strength and elasticity, I will use a reconstructor because I know that its small protein molecules will penetrate the hair and provide me with optimal results. However, if I need to address a porosity issue, I will use a protein-based conditioner due to its ability to coat the hair.
In essence, the difference lies in the function of each product as dictated by the size of the protein molecules: smaller, penetrative molecules = reconstructor; larger molecules that coat and fill in cracks = protein conditioner.