One easy way to avoid this problem altogether would be to, once the lift is done, keep all the OEM parts that are switched out (wheels, shocks, springs, ect) and if you ever have to bring the Jeep back to said dealer you could re-install them prior to going to the shop. This is assuming you only go with a BB 2" lift. If your having your lift work done by a local shop ask them ahead of time if they could help you out with this to avoid any problems with you dealer trying to pull a fast one and void said warranty.
That's quite a bit harder than it sounds.
First of all, this wouldn't actually undo any damage caused by your mods. So if the dealer suspects you've installed/uninstalled mods, they can still point to that as the reason to deny your claim. You can fight the denial if you like, but now "when the truth comes out" you're going to have to admit you're a liar who tried to trick them by uninstalling your mods.
Second and more immediately, if you want a shop to do the reinstall of old parts, they're going to want to get paid. Regardless of whether it's installing a new lift or reinstalling old parts, it's basically the same job. The $400 or so you pay to uninstall your budget boost--and the $400 or so you'd have to pay after the warranty work is done to reinstall the BB again--would likely cover quite a bit (or all) of whatever the potential warranty issue is.
You could of course do the uninstall at home, though even a BB is going to take you at least four hours. Then you'll need to take your Jeep in, hope to get the warranty work done, and then you'd need to spend another four hours reinstalling the mods. Ugh.
Third, mods often beget other mods. Your new tires probably won't fit once you remove the lift. So those would have to revert to stock too. So you'd be paying a shop or spending hours upon hours reverting everything you needed to revert.
Fourth and finally, some mods really aren't "undoable." Nobody would undo a regearing, for example. And if you've regeared, you probably CAN'T go back to stock tires without running insane RPMs everywhere.
So while this sounds good in theory and may work for some small mods, it's realistically not a viable option for serious mods.
My point was that if you can't afford to fix it without the warranty then you probably shouldn't mod it while it's under warranty.
But my point is that this seems to be conflating two issues. And once you parse them out, logic cuts the other way.
The first issue is: Should I mod at all? If you have no financial cushion to account for the impact of your mods, then I say you shouldn't mod at all--whether under warranty or not. This is so because you can't predict whether damage caused by mods will get warranty service or not and if the bill falls upon you, you can't afford it.
The second issue is: If I'm going to mod, then when should I do it? If you must mod, then I say logic dictates that you SHOULD do it while it's under warranty. This is so because then at least there is the CHANCE that if the mods cause damage, you could get warranty coverage. By contrast, if you wait until the warranty has expired to install the very same mods and they cause damage, then there is NO CHANCE you will get warranty coverage.
In other words, the only way to guarantee that you won't get any assistance repairing damage caused by mods is to make the mods outside of the warranty period.