In my opinion,
suspension mods are a little different than other mods. Not legally mind you, but in practice I think they are. Here's why- if you take a car that has been mildly lowered into a dealership, honestly there's a chance that they won't even notice that something has been done to the car. The only way that they'll notice if you've changed struts is if the body of the strut is a different color than the stock part. Other suspenion components are a bit more obvious, but really, how often do (well made, name brand, and PROPERLY INSTALLED)
suspension parts fail? It's a little different than engine mods.
Suspension modifications really don't malfunction, and if they should (barring out and out catastrophic failure) they won't damage other aspects of the car. A sagging spring is easily replaced and doesn't hurt anything else. All I'm saying is that
suspension changes are a pretty safe bet because they aren't necessarily immediately obvious and because if they cause problems or fail that failure is usually fairly isolated to that part alone.
Engine modifications, however, may affect more expensive, complex sustems. If you were to get a very aggressive tune for example (and I can't imagine someone selling you such a tune, but we'll play worst case scenario) it might cause plugs to foul or a rough idle, etc., problems that a Ford Dealership would not want to (and shouldn't have to) resolve. Furthermore, if you need a software update for your ECU and you have a program loaded to calibrate the new MAF in your cold air kit, you've potentially got a sticker situation on your hands. Not that the dealership should deny you service if there's no problem, it just complicates matters.
Long story short, it's kind of like a police officer. If a cop pulls you over and wants to pull everything out of your car to search it based on a nebulous "suspicion", he probably can. If he just writes you a warning for not having your license plate on the front or having a bad tail-light bulb, he can probably do that too. It's kind of up to the cop in the moment. Can you go to court and fight it out if worse comes to worse? Sure, but it probably won't ever get to that point as long as you're reasonable in you expectations about what they should and shouldn't cover in their warranty.
As for resale value, it's hard for me to think that anyone would pay significantly less (if at all) for a car that's been lowered a little or has a short throw shifter on it. Honestly, the probably aren't even going to notice unless they've a lot of other Mustangs to compare it to. My advice is to just enjoy the car and keep the stock parts on the shelf so if you need to reinstall them you can.