This has been debated a length on many a forums as well as here.
BUT here is my 10 cents. First off I'll admit to being new to tuning my cars personally but that said I still have a good opinion lol.
OK so as said already Ford "officially" doesn't want you to tune yourself, when they haven't "sanctioned" the tune. Sanctioned Ford tunes you ask, Yes you can buy warranted tunes from Ford Performance for the Mustang, and the 2 ST's. Before anyone asks, don't hold your breath for one for the Sport. All these years and they never made one for the SHO, so I don't think they ever will for the Sport. But I mention it to support the opinion that tuning can be done safely. What was already said in this thread about voiding warranty or not, I agree with. I will add that it would be more likely a denial of a said claim as opposed to a total voiding of warranty. Unless it is something as big as an engine replacement I expect Ford themselves probably wouldn't even question any claim, so it to me goes back to the dealer. The dealer can tell if it's been tuned if they care to, but unless they are total "goodie two shoes "? Or just jerks, what's really in it for them. If they don't think Ford will question the claim, why not just fix it and get paid. Especially true if the problem is in no way related to a tune.
OK, so are tunes really safe. Well this all depends. I expect any car can be tuned to an unsafe level, especially a turbo charged car. You can find stories of blown engines and voided warranties if you look hard enough. But circumstances are important in my opinion. I'll give you a great example. Last summer someone on this forum took his stock FuSpo to the track and almost lost to a tuned 2.0 fusion. This disappointed many people here. What the he ll. Our cars should be much better people cried. Well as it turned out, said guy in 2.0 Fusion blew his engine shortly thereafter and was crying loudly on the Internet how Ford voided his warranty. So what am I trying to say? Both due to driver behavior and a too aggressive tune any car can be pushed past its mechanical limits. This guy was drag racing his car regularly (not that there is anything wrong with that but it certainly stresses a car) and no 2.0 4 cylinder fusion has any business doing low/mid 13s 1/4. Not without accepting the risk.
Our car is built tougher than the 2.0 fusion. Our important bits are from the SHO, which has a big history of aftermarket tuning with great success. Our tunes and cars will but less stress on these same parts(less mass, less hp/tq). Livernois and Unleashed are very respected tuners, and it's not because they have a history of blowing people's motors. I expect if you ask them to push the limits and give you a faster custom tune they would probably do it, you are the customer. This is also why the argument about who is the best tuner based on track times will never be won. They can keep pushing the envelope if you/they really want to. But if you stick with their standard release tunes, and treat your car with some respect, my opinion is your likelyhood of failure isn't really any worse than stock. Your likelyhood of smiles is greatly increased however.
Also, I whole-heartedly agree with what Vert said regarding the boostmax in the other thread. I don't think anyone should necessarily feel safer using a product like that over a tune. Is it harder to prove you modified your car against the terms of the warranty? Maybe, but it isn't safer for your car. Read up on what it is doing. Like Vert said, it's tricking your car into thinking it's not doing something it is. If your car is tuned and something isn't right, the car will let you know, because it sees everything as it is. They don't "tune out" the normal safeguards.
All of this being said, I completely understand if someone doesn't want to mod their car. You do have to be able to accept some level of risk to do so. I personally don't think the risk is that high if you keep some of what I said in mind.
But I will also admit I don't get waiting till warranty is expired. If your going to accept some risk at some point why not take it when there's a good possibility to have it fixed for free under warranty. And why wait to get all your enjoyment out of the car till the car is already on a downward slide and the risk of failure is most likely greater due to all the wear and tear on the car. Stock or not your still driving your car harder than had you bought said 2.0 Fusion right?
You will have to return it to unmarry it with a nice bill!! 
