Yes its true if you go for the extended warranty - it has to be maintained by Lexus
The issue of indy vs dealer really does depend on the age of the vehicle. On a 4 year old+ car, probably better going to an indy. However, having said that, I think most people buying an F car would have the view that if you're skimping out on main dealer costs, what else has been missed? Thats with the proviso that the car is fairly new. I reckon most people understand that an older car is hardly ever taken to the dealer for a service.
Problem with files and invoices is that many can be easily forged, almost too easily. It only counts if you start ringing each one up and most don't even have any record/recollection of seeing the vehicle. Not saying Lexus stamps can't be forged but its all online and can be tracked down very easily.