I'm the FNG here but I've had direct experience with this, from both sides of the counter. I was a service writer but also an enthusiast car owner most of my life, so therefore, I'm going to weigh in. I've previously tuned most of my personal cars, relying on experienced tuners and never on canned tunes. I choose to take the risk, but it did recently bite me really good. I'll explain in just a bit.
First, I do not recommend anybody actually defend the position of hiding anything or lying, because it constitutes fraud against GM. Or at the very least, willfulness to commit fraud. Right now we have a vendor that just said it can't be detected, but I guarantee if handed a subpoena, their legal reaction would be to claim this product is solely for off-road use and they sold it as such, as-is as well. Nothing against any vendor who would do that, why stick your neck out when it could get cut off, right? But you have to be careful to believe it could not be detected. A investigation would prove them wrong very quickly.
If they (GM or the dealer) ask if the vehicle has been tuned, and you answer "no" but it has indeed been tuned, you basically immediately are now at fault of at least a misdemeanor. You, by enabling a warranty claim, are liable for fraud if you attempt it. It's the same as insurance claim in the eyes of the law. I'm not kidding. Do not forget that it is a lawful contract only if both parties are acting lawfully. You need to consider your legal position in matters like this. While GM or the dealership is not likely to prosecute, you are basically violating the law. And if you are using the law (Magnuson-Moss) to try and defend yourself while violating the law at the same time, I'm sure you can see how you would lose this battle instantly.
Now, that said, I mentioned that it bit me before so here's my story. I had a tuned Focus ST with basic bolt-ons, but putting out pretty good HP and a huge amount of torque over stock on that little snail of a turbo. It ran E30 and 91 tunes, but I never really raced it or pushed it more than maybe hopping on an on-ramp in a hurry. The tune mostly helped with drive-ability, mileage, and general feel of the car's power band, especially in hot desert weather which is a sore spot for the stock ST's programming. I even went so far as to make sure my tuner programmed for extra margin of error in extreme weather, by dropping to colder plugs and so on. The best intercooler available for the platform strapped on, it ran cool as a cucumber in 120 degree weather, and still made tons of power on E30, its fuel of choice in that hot weather.
Well it went down for a clutch failure at a dismally low 8k miles in, and the cause was undetermined. I hammered on Ford to cover it, citing that there's known failures of the slave cylinder leaking (and they did find fluid contamination), so they sent a district rep out to the car, and we went back and forth for weeks about it. I spoke with the dealer several times, Ford customer service and various managers up there a few times, but 29 days into the deliberation process they denied me completely, and I had to pay for a clutch job out of pocket, with barely 2 oil changes on the car. During this process, they asked what mods I had. I explained to them what I had done, why I had done it, and I was honest about it. Did this cost me the repair? I'm not certain. However, I am certain that if I had lied and then they found out, I would be a criminal. Would I be prosecuted? Probably not, in fact I'd say with 99.9% certainty that no they wouldn't. However that doesn't mean it would be appropriate or right for me to act that way. I act with integrity. I don't lie if I make a mistake at work. I don't lie or cheat to make my income. So you need to really think about that. In the end, the dealer felt bad for me (because they processed the repair assuming Ford would of course repair it under warranty, and they knew I wanted the car back asap so they took a chance and put it together without prior Ford approval), and they discounted the job substantially.
Honesty is the best policy, even if it isn't the cheapest. You guys remember that if I ever post anything in the classifieds, if you ever want a detail, or if you ever want me to build your audio system for you. We always must own up for our actions, seen and unseen.