Staphylococcus aureus pathogenicity islands (SaPIs) are a family of mobile genetic elements that exploit bacteriophages for their own production and spread. The SaPI host organism, S. aureus, has become progressively more virulent and resistant to antibiotics, and is continuously evolving. These rapid adaptation abilities imply a dynamic evolutionary capability likely driven by horizontal gene transfer, in which SaPIs play a key role. To date, three SaPI-encoded phage interference mechanisms which reduce phage propagation and promote dissemination of SaPIs, have been identified.These mechanisms reduce phage propagation, and are believed to promote the dissemination and persistence of SaPIs in the host population. One mechanism, mediated by cpm, directs production of small phage capsids that only accommodate SaPI genomes and not larger phage genomes. Yet, despite being classified as a phage interference mechanism, SaPIs lacking cpm seemed to display higher transfer frequencies than their respective wild-type elements, which suggested that cpm is not beneficial to SaPI. To account for this contradiction, we identified an issue with small capsid production and SaPI genome unit length, where direct insertion of a marker intended for monitoring SaPI transfer might have increased SaPI size beyond the small capsid packaging capacity, resulting in defective SaPI transducing particles. Thus, we propose that SaPI transduction frequencies may have been underreported. To test this hypothesis, we engineered a “size-conserved” marked SaPI, and compared transfer efficiencies of size-conserved against “wild-type” marked SaPI in transduction assays. Accordingly, we show that direct insertion of a marker indeed affected SaPI transfer adversely. Furthermore, we infected S. aureus at various multiplicities of infection to model SaPI-mediated phage interference across successive rounds of infection, which provides evidence that such mechanisms may play key roles in SaPI persistence. Therefore, previous SaPI constructs were unable to provide accurate representations of the dynamic relationship between SaPIs and phages in SaPI-mediated phage interference studies.