Welcome and congrats on the purchase.
I modify all of my cars extensively, but I've never had any issues with warranty repairs. The first and most important thing is to establish a great relationship with the service manager(s) at the dealership and the service guys in general. This starts with a good personal relationship so ask them about their kids, hobbies, etc.
Technically, as some people have sort of stated, the dealer has to prove the modification caused the problem, but in reality, if they did deny something, it would be up to you to prove it did NOT cause the problem. This is where the relationship with your service manager is so important. At the end of the day, they want to do warranty repairs because they get paid for them. At the same time, all of their warranty work is reviewed by a regional manager and other people, so the work needs to be justifiable.
One simple thing that you're already thinking about is to do mods that are easily removed. A tune is the simplest of these, but an air intake, exhaust, sway bars, and some other things don't take more than 20-30 minutes to swap out. And you don't need to remove EVERY mod EVERY time you take the car in for warranty work. Just remove things that are part of whatever part/system you're requesting warranty work on. With regards to modifying your suspension, that's one thing where you're highly unlikely to have any warranty issues, so I don't know why you're so hesitant to change it. The suspension is a pretty basic mechanical system with very little that can go wrong (warranty-wise), so it should be the one thing you modify that you should NOT be concerned about.