Patient-specific flanged acetabular components are utilized to treat failed total hip arthroplasties with severe acetabular defects. We previously developed and published a finite element model that investigated the impact of hip joint center lateralization on construct biomechanics during gait conditions. This model consisted of a patient-specific implant designed to address a superior-medial defect created in a standard pelvic geometry. This study aims to utilize the same model and examine how cortical shell thickness and ischial cancellous bone density affect the strain distribution in the bone and bone–implant micromotion. Using published studies and bone density analyses of patients who had undergone total hip arthroplasties with flanged acetabular components, we established a thickness range for the cortical shell (1.5, 1, and 0.75 mm) and two levels of ischial cancellous bone density (100% and 25%). We compared the resulting bone strains against the fatigue strength of the bone (0.3% strain) as a criterion for local bone failure and the bone–implant micromotion against the threshold associated with bone ingrowth (20 µm). A thinner pelvic cortical shell and lower ischial cancellous bone density increased areas of bone at risk of failure, particularly at the ischial screws (from 6% to 38%), and decreased areas compatible with bone ingrowth. These findings agree with our clinical knowledge that compromised ischial bone and inadequate ischial fixation negatively impact the survivorship of flanged acetabular components. This series establishes our modeling approach of a computational model that can be utilized to guide implant design to best treat unique acetabular defects.