No, the proteins were on the Y that were farther than the chicken. It was not evident on the match as they were not identified as such on the comparison lines. The opposum both X and Y are farther away than the chicken and they have less identities than the chicken.
Again I'm not an expert on this area (the sheer volume of results coming from genomics is intimidating), but my guess is the y-linked proteins are not expressed, and therefore aren't subject to significant evolutionary pressure, so they diverge rapidly. S4, where it is on X or on a somatic chromosome, seems to be very highly conserved. 4 mutations between birds and mammals, and highly conservative mutations at that, over 200 amino acids, is very stable indeed...which makes sense for a ribosomal protein, I suppose.