So after I talked to the guy in the store I called up applecare for a second opinion. The guy on the phone said he couldnt give me any information apart from the advisory (a standard page on their website). That was yesterday (15/07/2013). Today, I got a call from the same guy who said that he could get me a supervisor for some further discussion (which is awesome as I was not expecting a call at all, especially not an elevation of the issue).
The supervisor gave me some basic guidance agreeing with me and (from what he implied) talked to the legal department, which corroborated my initial feelings about this process (that the apple store manager was wrong). Following this he passed my case on to customer relations, who assigned me a case worker and who will look into the issue further. I am expecting a call back soon.
This being the case I have chosen to stay a course of action dealing with the store directly. However, I will eventually need to deal with them again if a resolution has me requiring a repair/ replacement, though it must be said I am kinda disenfranchised with macbook pros in general at the moment.
I have to say, that the calls I have had today are typical of what I have experienced with Apple customer support in general, which is quick, efficient and personal customer care that leaves everyone happy. I am not sure if it was just the manager of that store having an off day, of if he didnt understand the policy but the time I had with him was an outlier and I am glad that Apple is seeking to resolve the case.
Will update as this goes on.