I have had the same work done on my car following a breakdown on the M18 the RAC did some temporary fix but only lasted a few miles eventually the car was recovered to Lexus Sheffield. It was with them for a week in this time they fit modified pistons and rings, did a de-coke fit EGR valve, an ECU and catalytic converter. Excellent service from Gary and his team at Sheffield. It was explained to me that this can happen at any time with early engines mine is on 57 plate but who knows when the engine was built, regardless of how many miles the car has done What happens is oil passes the piston rings causing a build up of carbon in the cylinders any un-burnt oil goes into the EGR valve to cause a blockage and then into the catalytic converter damaging that.
At first my MPG was poor around mid 30 and I was getting 42 before my breakdown, it is understandable that after such extensive work the engine will be tight and will take time to bed in. I have now covered about 1000 miles since the engine rebuild and the MPG has steadily risen and is now at 40, I think it is a case of gentle driving and you should see an improvement given time.
My car was out of warranty and the work was done free of charge, do not forget that this engine in guaranteed for 100k.
Merv