Why is 5S-rRNA is different from other rRNAs in place of transcription and usage of RNA polymerase?
The three RNA polymerases (RNAPs) are very similar to each other, yet not identical. As described in this article, there are subunits that are specific for each type of polymerases. 


  In addition to providing unique substrates that polymerase-specific subunits bind to give each of the RNAPs their specific functionality, the two largest subunits also shape the active site cleft of the enzymes where the transcription reaction occurs. 


The results of the linked article also claim that even though the cleft loops are conserved regions, there are significant length differences between the three polymerases.

Also rRNA gene is similar to the tRNA genes and they differ from other genes in the recruitment of the polymerases. "Traditional' promoters are located upstream the start site, while 5s rRNA gene and tRNA genes have one and two boxes respectively that recruits RNAPIII.


  The 5s rRNA and tRNA genes have promoters within the coding region of the gene. 


source: http://mol-biol4masters.masters.grkraj.org/html/Gene_Structure5C-Eukaryotic_Promoter_Structure_for_RNA_Polymerase_III.htm

Here are two images form the linked page:




Edit:

In this article it is described that 5s RNA genes have translocated severeal times throughout evolution, and on of the mechanisms for this could be analogous of the second class of SINE elements, that contain internal RNAP III promoters, and are derived form tRNA (this could also indicate the similar structure to tRNA genes).

From this good review Evolution of multisubunit RNA polymerases in the three domains of life
 I'd like to take one short quote that might help:


  ...The structure and function of some of these factors are conserved across the three domains, whereas some non-homologous factors show an intriguing level of structural and functional similarity, suggesting that convergent evolution has led to alternative means of facilitating the same process.