Firstly, I cannot believe Premier Guarantee Warranty is expecting you to get a quote for the clear cut defect to be investigated.
You will also have to pay an excess on the cost of any claim too. (£1500 I think)
From what you say it could be anything or a combination of things.
Cavity trays missing damaged, full of debris, ends not turned up.
Weep holes missing blocked, in wrong place.
Flashing issue, falling out, displaced by wind, insufficient laps, damaged.
Possibly flat roof is failing.
One thing that stands out is, the home is over 2 years old and only now this has become an issue.
This points to weather/storm damage which is the excuse I expect Premier will use to get out of doing anything at all.
My advice would be to get a professional inspector to find out what is causing the leak, before trying to appoint a builder to fix it.
Finally who was the housebuilder?