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Legally, it doesn't take you off the hook at all. Nothing in the ADA requires that an employer accept and not terminate in a situation where a person has a positive drug test.
The point of their company policy is that if you were to voluntarily come forward before you believe you are going to get caught and ask the employer for the opportunity go to drug counseling/rehabilitation, then legally you'd be protected from discrimination for going to rehab. However, if you test positive and THEN ask the employer for time off to go to rehab, it's too late then. You didn't come forward due to the desire to go to rehab, but rather, because you knew you'd be failing a test.
No, I do not believe the employer here is intending this as a loophole for smokers. In terms of loop holes, everyone always asks about that but really they don't exist. I think people get the idea from television or from what they'd heard from friends, but law isn't as hyper-technical as people have been led to believe. Random drug testing is highly unregulated, the opposite of what you'd expect.
If you know you will be testing positive, then I certainly think that you would be in stronger position by going forward before they come to you. You can even raise the issue of their policy wording. That may give them pause and cause them to extend to you a second chance. However, if they choose not to, their policy wouldn't give you any means of suing them for wrongful termination.
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