The police don't hassle folks over window glass unless, in your state, the Gestapo is particularly against cracked windshields. (Tints are a different question). The legality of non-approved window glass and its ramifications lie elsewhere.
For example, if you install Lexan windows and you are in an accident, any liability arising from the use of non-DOT approved equipment lies with you, not with the manufacturer or any other party involved, including your insurance company. If you are trapped and can't get out of the car, that's your problem, including any bodily injuries that subsequently arise because you could not escape the vehicle. If your window pops out and cuts a bystander in half, that is going to be your problem, and your insurance company won't pay up because the product was installed in violation of DOT regs. If you are independently wealthy and don't much care, you may do as you please. If you are building an off-road toy, you can build as you wish. But if you rely on insurance to cover you in the event of liability, you risk voiding your coverage by using Lexan in any of the passenger cabin windows.