Spoken to a senior Apple technical advisor who has told me to take the laptop to a Premium Apple service provider for a 2nd opinion, they have wavered the £99 diagnostic fee. I'll take it in next weekend.
Spent 30 minutes convincing them at it wasn't a software issue.
Update -
So I took the MBP to the Premium service provider. Gave the repair reference number which Apple provided and the serial number. They bought up all the information and the code for them to charge back to Apple with. Result! The store ran the same test which the genius guy used in the Apple Store, which then advised to run the GPU one. At this point I left. They said someone would be in contact with me over the next couple of days with an update.
A couple of days later I received a call asking me to come in and collect my laptop. They couldn't find any issue and had passed their tests and as a added bonus I would need to pay the inspection fee as they were unable to charge their inspection fee back to Apple with the code Apple provided. I politely said I would call my contact in Apple first and see what now needs to be done now as I wasn't willing to pay the inspection fee due to Apple agreeing that they would cover it.
A few phone calls later with a manager within Apple over the course of a few days. I was keen to express how disappointed I am with Apple, no one seems to believe me that there's an issue even though I have provided a number of pictures and videos of the issue and it seems that unless this GPU test fails no one is willing to do anything more than just give me the laptop back.
Toni from Apple, who has been dealing with my case, she has been great though, listening and trying to provide a solution. Calling the service provider store and arranging everything only calling me to give me an update.
So now Apple have agreed to replace the Logic Board. Email confirmation has been passed to the service provider and the store has now ordered a replacement, which should be here tomorrow. Finally!
Hopefully by this time next week I should have a fully working MacBook Pro again.
My advise for anyone else who has experience this problem. Even though Apple's test passes, keep on at Apple, get a manager to own the case, take as many pictures and videos of the issue and report them to technical support every time. Keep a detailed history, how many times you've had to call, what happened by whom.