My main point would be that if it is faulty then either the garage or warranty should cover it regardless of what their margin is.
If it has been parked up for a while then it is feasible the turbo actuators could be sticky, or it could genuinely need new turbos, you need to know what fault codes it has which will have been logged which may give you some idea.
Did you notice power problems or limp mode when the light came on or when did it occur?
if you trust the garage and they are genuinely trying to put it right then its a maybe, replacing the turbos is expensive, if you can get them replaced with brand new genuine units for little outlay then it is probably the most expensive problem you could face as transmissions seem pretty solid as do the engines but do yourself some research.
The warranty companies are genuinely pretty ruthless in what they do and don't cover and i would imagine they will try and avoid paying anything if they can but again i don't know what cover you have.
i purchased my 04 at about £1000 - £1500 under market value and then went on to rebuild the transmission, the front suspension (failed when i arrived home from collecting it), all the front and rear suspension arms and bushes, rebuilt the timing chain and vanos, new battery, new water pump and a whole load of other stuff i have forgotten so my bargain price diminished into negative equity quite rapidly. That is not to say i wouldn't have had to replace all those things if i had paid full market price.
I would be looking at what service history the car has, although mine had been fabricated as somebody obviously made a mistake when filling in all the mileage for the different services as then had to go back and change them.
They are a delightful vehicle when working well, the only reason they normally get sold is you like them so much and have a lot of money so you can afford to upgrade to a newer one, or its fooked and you want to cut your losses and pass it on to somebody else to fix up. The third reason normally involves child birth of some sort and your driving for fun is over