Sorry to keep posting, but I keep learning and encountering different behavior!
I've just installed a fresh copy of XC5 on a hosted account with TSS, previously I was working on my local Windows machine. Everything is working differently than before! I packed up the custom skin module and uploaded it to the hosted site. Then I enabled the Market Price module, and setup the market price on the Macbook. Completely different results!
https://docs.google.com/file/d/0B46HNJGXAQ6gb3RlQXpzRlZsSjA/
So I am starting to understand your duplicate content. Its just not happening at all for me on my local machine.
Okay so now I have removed the skins/default/en/modules/XC/CustomSkin folder, and it got rid of one of my duplicates.
Then I removed skins/custom_skin/default/en/modules and that got rid of another.
Now I just have two files:
skins/custom_skin/default/en/items_list/product/grid.product.market-price.tpl
skins/custom_skin/default/en/items_list/product/grid.product.our-price.tpl
With the same content as above. Everything is working perfectly. I'm going to test overwriting a file with the custom skin on this hosted box. It went perfectly, I created skins/custom_skin/default/en/items_list/product/parts/common.product-price.tpl and added the text Hello World. It worked perfectly, overriding the default template. You can see it all working for the time being here:
http://xcartnext.com/
I've attached my copy of the Custom skin module to this post. I renamed it to zip from tar, just so I could upload it. rename it .tar when you download it.