One reason to use buffer sites is to protect your money sites from the potentially harmful effects of mass link building. By doing so, you can worry less about red flags being raised for too high a link velocity and for the low quality of these links.
It is also partly to do with crawl rate - by having 500 links pointing to site A, there are many entry points for Google's spider to flow through from the crappy backlink to site A and then to your money site. Thus your money site might get a higher crawl rate. In theory, having a page on your site crawled regularly should benefit its rankings ever so slightly and it will certainly help any changes you make get cached quickly. If site A points to the homepage of your money site then it should mean new content gets crawled more quickly then if you just had site A without the 500 backlinks in your 2nd tier.
But you will not get the power of the 500 links - they will have very low power anyway if, as I am assuming, you are building them using a tool like GSA or SENuke. Site A will get some power from the 500 links, but it's as much to do with creating paths for spiders as it is "juice".