The dealer is simply taking the position that since the vehicle was involved in an accident (which they presumably don't know the details of), they need to do significant diagnosis to find the problem, and won't be sure what caused the problem until they find it.
This doesn't mean they will charge you. It simply means they're asking you to promise to cover their time spent on diagnosis in the event they find the problem and it isn't warrantable. It sounds like they have some idea what direction they're headed-- i.e., they know what type of problem they have (e.g. no power to crank sensor) but still need to find out why that is occurring, and it's not going to be very simple.
If they do tell you it's accident related, be prepared to submit any needed repairs to an appropriate insurance company. If the insurance company and dealer disagree, they'll likely work it out between them. If there's no insurance involved, they should be able to explain to or show you why the problem is related to the accident.