As far as I know Shimano is still doing their best to stand behind their products. the fact is if too many people abusing the warranty, the tighter the service will be. if the rod was broken because of abuse, miss use or accident, don't try to get it replace, sure they will take it back and give you a new one, but when it starting to hurt their bottom line, the next guy with a real "defects" rod may have a hard time to get service.
About retailer doing over the counter, it is up to the store, best is take it back to where you brought it since the retail should fulfills the after sells service. If the customer choose to use another retailer, a service charge should be apply but again it is up to the store. I was working in the store yesterday and a customer came in and mentioned his crucial rod broke and the store he purchase the rod from is no longer in business, he was not sure what to do, we took the rod and told him we will sent out the rod for replacement, no charge.