A bit of miss information here, lets try and clear this up.
Infiniti can only deny warranty if a modification is somehow related to the issue that they are investigating and prove it, this means if you have an after-market exhaust
and you're AC stops working Infiniti has to honor the warranty and repair the AC as the modification has no impact on the AC system.
Where as if you replaced your suspension with new coil-overs and you end up having to replace a bushing or end-link then that would not be covered.
In the case of an ECUtek/JB4 tune things are a bit more complicated as it effects so many systems.
Warranty can be denied for both types of tunes if discovered;
JB4 - Modifies how the car reads the incoming signals and effectively tricks the car into thinking it can run more boost,
this makes it very hard to detect and would require a technician dig through log files to prove the car is behaving in a particular
manner.
However if a technician sees a JB4 unit installed the car can be flagged or if they are actively investigating an issue
and are looking at the log files they can see
ECUTek - Effectively flashes the ECU with the version the tuner provides, this process then updates a counter
which Infiniti can very easily check any time the car is in for service and compare against their records to see if it matches what they have on file.
However as far as I'm aware Infiniti does not actively check this counter unless they suspect a tune is present and the cause of an issue,
where as someone like Audi will check their cars every time they go in for service even if it's just for an oil change.
Ultimately your experience will depends on the dealership you are going to and it's staff, some will see small indications and look
the other way and other shops despise any type of modification and will make your life miserable.
Get to know your shop before doing any big changes and most important be willing to pay out of pocket if things go south.