Obviously the warranty T&Cs will need to be read carefully but in my experience (not with Lexus) warranty is not voided by modifications but if the mod can be shown to be the cause of the claim or be involved in the failure of another component, the warranty will not be honoured on those components.
If one were to modify the exhaust and a wheel bearing failed, that would be covered. If one were to modify the suspension and the wheel bearing failed, one might have a fight on one's hands..
It can be a grey area and gives the policy provider an opportunity to wriggle out of coughing up.