If you are that concerned about using a template, then don't use one--you have that choice. I haven't read anything about templates interfering with the new search engine--please share your info/facts from ebay (not just some sellers conspiracy theory). I have actually seen an increase in sales this month, so I know that my templates aren't interfering with search results. I make sure my keywords and item specifics are up to date, and I always use the ebay gallery image option (I'm not sure why you are saying you have to add them on ebay?) Until my sales start to tank, I will continue doing what I've been doing (since it's obviously working just fine). If or when ebay comes right out and says not to use templates, then I will not list with them.
Ebay offers templates to sellers too, and why would they do that if it directly interfered with their own search machine?