Update on this - left the car with VW while I went on holiday, got it back today and all sorted (touch wood!), it was the fuel lines rattling but also noises coming from the ECU mount and air vents which have all been sorted. Certainly sounds much quieter now!
They also found my electronic differential was leaking oil (with swarf found in it) and was opened up and found to be distorted inside (I was told a manufacturing error was likely the cause of this) so a new one was replaced all under warranty. They had previously replaced the seals on the diff when they found an oil leak on it so when they saw it leaking again just 2 weeks later they investigated it further.
Needed a few trips to the dealer but it seems like everything is finally sorted, the service advisor and technician at the dealer (High Wycombe) were very helpful and friendly. My car was on PCP with VWFS so I wrote them an email about all the issues and various trips to the dealer in the last month and they have refunded me £400 which I was also quite pleased about!