Seurat FindMarkers() output, percentage
Your interpretation of pct.1 and pct.2 is misguided. If pct.1 == 1, the given gene was detected in all of the cells. This carries no information about high expression or low expression in the cell, just that it was detected. avg_logFC is the indication of expression levels. So your expectation, that 


  "we would instead expect the genes to be expressed at high levels in the cells within the cluster but at low levels in cells not within the cluster"


holds true, as indicated by the positive avg_logFC and significant p-values of the listed RP genes.

Seurat use nautral log, so the FC of RPS6 in cluster 0 vs. all other clusters indicated is 2.718281828459^.55947=1.750.



Seurat FindMarkers() documentation.