The areas that you leave without peening may have either compressive or tensile stresses (residual) from earlier processing (cutting, grinding, turning etc). If those stresses are tensile then you could expect fatigue failures with applied tensile stress. If those residual stresses are compressive you would expect longer fatigue life, depending upon stress levels (applied versus the residual).
The above is considering large areas, not the small areas in a 80% peening application. In this case the dents are evenly distributed and only very small areas are left "original". These untreated areas are typically smaller then the peening dents. However, since the affected zone for peening, below the surface, is generally three times the area seen on the surface, there is no problem. The sub-surface peened zone will offer complete protection underneath the dents seen on the surface that appear to have gaps from dent to dent.
