Dealers will always put on new wheels unless completly unmarked. Tyres need to be 4mm + for Lexus approved and they will put on OEM ones.
40k service is not that expensive, not when the dealer is getting parts at trade prices and their own people are doing the work.
Lexus dealers have a large difference between trade-in and retail due to cost of service/wheels/tyres/respray etc. but they still make a good profit so try and knock them down. However be aware that there are alot of people who will pay the asking price so the dealer may just hold out.
Leased/company cars. This is a difficult call, I know many people who abuse their company cars but then others treat them like their own. The IS is reliable so if it's got full history, which it will have from a dealer, and it comes with a one year warranty then you shouldn't have many problems.